######################################################################## # # # AlphaFold Protein Structure Database Dictionary (V1) # # # ######################################################################## data_mmcif_af.dic _datablock.id mmcif_af.dic _datablock.description ; This data block holds the AlphaFold Protein Structure Database dictionary. This is based on data categories collated from the PDBx/mmCIF dictionary (http://mmcif.wwpdb.org) and the Model Archive (MA) dictionary (https://github.com/ihmwg/MA-dictionary). ; _dictionary.title mmcif_af.dic _dictionary.datablock_id mmcif_af.dic _dictionary.version 1.0.2 # loop_ _dictionary_history.version _dictionary_history.update _dictionary_history.revision 1.0.0 2021-11-24 ; Changes (jt) + Initial collation of mmcif_pdbx and mmcif_ma categories ; 1.0.1 2021-11-25 ; Changes (jt) + Corrections made to parent:child links and mandatory items ; 1.0.2 2021-11-25 ; Changes (jt) + Made corrections in light of Gemmi validation of AF model files. ; ######################### ## CATEGORY_GROUP_LIST ## ######################### loop_ _category_group_list.id _category_group_list.parent_id _category_group_list.description ## 'inclusive_group' . ; The parent category group containing all of the data categories in the macromolecular dictionary. ; 'atom_group' 'inclusive_group' ; Categories that describe the properties of atoms. ; 'audit_group' 'inclusive_group' ; Categories that describe dictionary maintenance and identification. ; 'chem_comp_group' 'inclusive_group' ; Categories that define the chemical structure and nomenclature of the momoners and ligands in the experiment. ; 'chem_comp_dictionary_group' 'inclusive_group' ; Categories defining chemical structure and nomenclature of the momoners and ligands used in the Chemical Component Dictionary. ; 'citation_group' 'inclusive_group' ; Categories that provide bibliographic references. ; 'computing_group' 'inclusive_group' ; Categories that describe the computational details of the experiment. ; 'database_group' 'inclusive_group' ; Categories that hold references to entries in databases that contain related information. ; 'entity_group' 'inclusive_group' ; Categories that describe the unique chemical and molecular entities. ; 'entry_group' 'inclusive_group' ; Categories that pertain to the entire data block. ; 'pdbx_group' 'inclusive_group' ; Categories which have been added to support the data archiving and exchange for the Protein Data Bank. ; 'ma_group' 'inclusive_group' ; Categories that describe the modeling extension dictionary. ; 'struct_group' 'inclusive_group' ; Categories that contain details about the experimental structure. ; #################### ## ITEM_TYPE_LIST ## #################### # # # The regular expressions defined here are not compliant # with the POSIX 1003.2 standard as they include the # '\n' and '\t' special characters. These regular expressions # have been tested using version 0.12 of Richard Stallman's # GNU regular expression library in POSIX mode. # # ############################################################################## loop_ _item_type_list.code _item_type_list.primitive_code _item_type_list.construct _item_type_list.detail atcode char '[][ _(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; Character data type for atom names ... ; code char '[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words ... ; ucode uchar '[][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*' ; code item types/single words (case insensitive) ... ; line char '[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; char item types / multi-word items ... ; uline uchar '[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; char item types / multi-word items (case insensitive)... ; text char '[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*' ; text item types / multi-line text ... ; int numb '[+-]?[0-9]+' ; int item types are the subset of numbers that are the negative or positive integers. ; float numb '-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?' ; float item types are the subset of numbers that are the floating numbers. ; name uchar '_[_A-Za-z0-9]+\.[][_A-Za-z0-9%-]+' ; name item types take the form... ; yyyy-mm-dd char '[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]' ; Standard format for CIF dates. ; ec-type char '([1-7]((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?[0-9]?)|(.-)))(([ ]*,[ ]*)([1-7]((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?)|(.-))((.[1-9][0-9]?[0-9]?)|(.-))))*' ; Approximate format of Enzyme Commission EC number. 1.2.3.4 with optional parts. ; ##################### ## ITEM_UNITS_LIST ## ##################### loop_ _item_units_list.code _item_units_list.detail 'angstroms' 'Angstroms (metres * 10^(-10)^)' '8pi2_angstroms_squared' '8pi^2^ * Angstroms squared (metres * 10^(-10)^)^2^' ################## ## SUB_CATEGORY ## ################## loop_ _sub_category.id _sub_category.description 'cartesian_coordinate' ; The collection of x, y, and z components of a position specified with reference to a Cartesian (orthogonal Angstrom) coordinate system. ; 'mm_atom_site_auth_label' ; The collection of asym id, atom id, comp id and seq id components of an author's alternative specification for a macromolecular atom site. ; 'mm_atom_site_label' ; The collection of alt id, asym id, atom id, comp id and seq id components of the label for a macromolecular atom site. ; ######################################################################## # # # MMCIF PDBX DERIVED DICTIONARY CATEGORIES # # # ######################################################################## ########### ## ENTRY ## ########### save_entry _category.description ; There is only one item in the ENTRY category, _entry.id. This data item gives a name to this entry and is indirectly a key to the categories (such as CELL, GEOM, EXPTL) that describe information pertinent to the entire data block. ; _category.id entry _category.mandatory_code no _category_key.name '_entry.id' loop_ _category_group.id 'inclusive_group' 'entry_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _entry.id AF-Q8W3K0-F1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entry.id _item_description.description ; The value of _entry.id identifies the data block. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_entry.id' _item.category_id entry _item.mandatory_code yes _item_aliases.alias_name '_audit_block_code' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code save_ ############### ## ATOM_TYPE ## ############### save_atom_type _category.description ; Data items in the ATOM_TYPE category record details about the properties of the atoms that occupy the atom sites. ; _category.id atom_type _category.mandatory_code no _category_key.name '_atom_type.symbol' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; loop_ _atom_type.symbol C N O S ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__atom_type.symbol _item_description.description ; The code used to identify the atom species (singular or plural) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underscore with the additional proviso that digits designate an oxidation state and must be followed by a + or - character. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_type.symbol' atom_type yes '_atom_site.type_symbol' atom_site yes _item_aliases.alias_name '_atom_type_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code loop_ _item_examples.case 'C' 'Cu2+' 'H(SDS)' 'dummy' 'FeNi' save_ ################## ## AUDIT_AUTHOR ## ################## save_audit_author _category.description ; Data items in the AUDIT_AUTHOR category record details about the author(s) of the data block. ; _category.id audit_author _category.mandatory_code no _category_key.name '_audit_author.pdbx_ordinal' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; loop_ _audit_author.name _audit_author.pdbx_ordinal "Jumper, John" 1 "Evans, Richard" 2 "Pritzel, Alexander" 3 "Green, Tim" 4 "Figurnov, Michael" 5 "Ronneberger, Olaf" 6 "Tunyasuvunakool, Kathryn" 7 "Bates, Russ" 8 "Zidek, Augustin" 9 "Potapenko, Anna" 10 "Bridgland, Alex" 11 "Meyer, Clemens" 12 "Kohl, Simon A. A." 13 "Ballard, Andrew J." 14 "Cowie, Andrew" 15 "Romera-Paredes, Bernardino" 16 "Nikolov, Stanislav" 17 "Jain, Rishub" 18 "Adler, Jonas" 19 "Back, Trevor" 20 "Petersen, Stig" 21 "Reiman, David" 22 "Clancy, Ellen" 23 "Zielinski, Michal" 24 "Steinegger, Martin" 25 "Pacholska, Michalina" 26 "Berghammer, Tamas" 27 "Silver, David" 28 "Vinyals, Oriol" 29 "Senior, Andrew W." 30 "Kavukcuoglu, Koray" 31 "Kohli, Pushmeet" 32 "Hassabis, Demis" 33 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit_author.name _item_description.description ; The name of an author of this data block. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; _item.name '_audit_author.name' _item.category_id audit_author _item.mandatory_code yes _pdbx_item.name '_audit_author.name' _pdbx_item.mandatory_code yes _pdbx_item_type.name '_audit_author.name' _pdbx_item_type.code author _pdbx_item_description.name '_audit_author.name' _pdbx_item_description.description 'List people responsible for the contents of this entry. Hyphens, apostrophes and blank spaces are allowed in the last names. Special characters and character modifiers should not be used.' _item_aliases.alias_name '_audit_author_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A' _pdbx_item_examples.name '_audit_author.name' _pdbx_item_examples.case 'Jones, T.J.' _pdbx_item_examples.detail . save_ save__audit_author.pdbx_ordinal _item_description.description ; This data item defines the order of the author's name in the list of audit authors. ; _item.name '_audit_author.pdbx_ordinal' _item.category_id audit_author _item.mandatory_code yes _item_type.code int loop_ _item_examples.case 1 2 3 save_ ################### ## AUDIT_CONFORM ## ################### save_audit_conform _category.description ; Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant. ; _category.id audit_conform _category.mandatory_code no loop_ _category_key.name '_audit_conform.dict_name' '_audit_conform.dict_version' loop_ _category_group.id 'inclusive_group' 'audit_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - any file conforming to the current CIF core dictionary. ; ; _audit_conform.dict_name cif_core.dic _audit_conform.dict_version 2.3.1 _audit_conform.dict_location ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__audit_conform.dict_location _item_description.description ; A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms. ; _item.name '_audit_conform.dict_location' _item.category_id audit_conform _item.mandatory_code no _item_aliases.alias_name '_audit_conform_dict_location' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__audit_conform.dict_name _item_description.description ; The string identifying the highest-level dictionary defining data names used in this file. ; _item.name '_audit_conform.dict_name' _item.category_id audit_conform _item.mandatory_code yes _item_aliases.alias_name '_audit_conform_dict_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ save__audit_conform.dict_version _item_description.description ; The version number of the dictionary to which the current data block conforms. ; _item.name '_audit_conform.dict_version' _item.category_id audit_conform _item.mandatory_code yes _item_aliases.alias_name '_audit_conform_dict_version' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text save_ ############### ## CHEM_COMP ## ############### save_chem_comp _category.description ; Data items in the CHEM_COMP category give details about each of the chemical components from which the relevant chemical structures can be constructed, such as name, mass or charge. ; _category.id chem_comp _category.mandatory_code no _category_key.name '_chem_comp.id' loop_ _category_group.id 'inclusive_group' 'chem_comp_group' 'chem_comp_dictionary_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; loop_ _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.type "C3 H7 N O2" 89.093 ALA y ALANINE ? "L-PEPTIDE LINKING" "C6 H15 N4 O2" 175.209 ARG y ARGININE ? "L-PEPTIDE LINKING" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE ? "L-PEPTIDE LINKING" # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__chem_comp.formula _item_description.description ; The formula for the chemical component. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. ; _item.name '_chem_comp.formula' _item.category_id chem_comp _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'C18 H19 N7 O8 S' save_ save__chem_comp.formula_weight _item_description.description ; Formula mass in daltons of the chemical component. ; _item.name '_chem_comp.formula_weight' _item.category_id chem_comp _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__chem_comp.id _item_description.description ; The value of _chem_comp.id must uniquely identify each item in the CHEM_COMP list. For protein polymer entities, this is the three-letter code for the amino acid. For nucleic acid polymer entities, this is the one-letter code for the base. ; loop_ _item.name _item.category_id _item.mandatory_code '_chem_comp.id' chem_comp yes '_atom_site.label_comp_id' atom_site yes '_entity_poly_seq.mon_id' entity_poly_seq yes '_struct_conf.beg_label_comp_id' struct_conf yes '_struct_conf.end_label_comp_id' struct_conf yes _item_type.code ucode loop_ _item_examples.case 'ALA' 'VAL' 'DG' 'C' save_ save__chem_comp.mon_nstd_flag _item_description.description ; 'yes' indicates that this is a 'standard' monomer, 'no' indicates that it is 'nonstandard'. Nonstandard monomers should be described in more detail using the _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and _chem_comp.mon_nstd_details data items. ; _item.name '_chem_comp.mon_nstd_flag' _item.category_id chem_comp _item.mandatory_code no _item_type.code ucode _item_default.value no loop_ _item_enumeration.value _item_enumeration.detail no 'the monomer is nonstandard' n 'abbreviation for "no"' yes 'the monomer is standard' y 'abbreviation for "yes"' save_ save__chem_comp.name _item_description.description ; The full name of the component. ; _item.name '_chem_comp.name' _item.category_id chem_comp _item.mandatory_code no _item_type.code text loop_ _item_examples.case 'alanine' 'valine' 'adenine' 'cytosine' save_ save__chem_comp.pdbx_synonyms _item_description.description ; Synonym list for the component. ; _item.name '_chem_comp.pdbx_synonyms' _item.category_id chem_comp _item.mandatory_code no _item_type.code text _item_examples.case ATP _item_aliases.alias_name '_chem_comp.ndb_synonyms' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__chem_comp.type _item_description.description ; For standard polymer components, the type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap and monomers with some type of C-terminal (or 3') cap. ; _item.name '_chem_comp.type' _item.category_id chem_comp _item.mandatory_code yes _item_type.code uline loop_ _item_enumeration.value _item_enumeration.detail 'D-peptide linking' . 'L-peptide linking' . 'D-peptide NH3 amino terminus' . 'L-peptide NH3 amino terminus' . 'D-peptide COOH carboxy terminus' . 'L-peptide COOH carboxy terminus' . 'DNA linking' . 'RNA linking' . 'L-RNA linking' . 'L-DNA linking' . 'DNA OH 5 prime terminus' . 'RNA OH 5 prime terminus' . 'DNA OH 3 prime terminus' . 'RNA OH 3 prime terminus' . 'D-saccharide, beta linking' . 'D-saccharide, alpha linking' . 'L-saccharide, beta linking' . 'L-saccharide, alpha linking' . 'L-saccharide' . 'D-saccharide' . 'saccharide' . 'non-polymer' . 'peptide linking' . 'peptide-like' . 'L-gamma-peptide, C-delta linking' 'Iso-peptide linking L-gamma peptide' 'D-gamma-peptide, C-delta linking' 'Iso-peptide linking D-gamma peptide' 'L-beta-peptide, C-gamma linking' 'Iso-peptide linking L-beta peptide' 'D-beta-peptide, C-gamma linking' 'Iso-peptide linking D-beta peptide' 'other' . save_ ############## ## CITATION ## ############## save_citation _category.description ; Data items in the CITATION category record details about the literature cited as being relevant to the contents of the data block. ; _category.id citation _category.mandatory_code no _category_key.name '_citation.id' loop_ _category_group.id 'inclusive_group' 'citation_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _citation.book_publisher ? _citation.country UK _citation.id 1 _citation.journal_full Nature _citation.journal_id_ASTM NATUAS _citation.journal_id_CSD 0006 _citation.journal_id_ISSN 0028-0836 _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.title "Highly accurate protein structure prediction with AlphaFold" _citation.year 2021 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__citation.book_publisher _item_description.description ; The name of the publisher of the citation; relevant for books or book chapters. ; _item.name '_citation.book_publisher' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_book_publisher' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'John Wiley and Sons' save_ save__citation.country _item_description.description ; The country/region of publication; relevant for books and book chapters. ; _item.name '_citation.country' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_country' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.id _item_description.description ; The value of _citation.id must uniquely identify a record in the CITATION list. The _citation.id 'primary' should be used to indicate the citation that the author(s) consider to be the most pertinent to the contents of the data block. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_citation.id' _item.category_id citation _item.mandatory_code yes _item_aliases.alias_name '_citation_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code loop_ _item_examples.case 'primary' '1' '2' save_ save__citation.journal_full _item_description.description ; Full name of the cited journal; relevant for journal articles. ; _item.name '_citation.journal_full' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_full' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _item_examples.case 'Journal of Molecular Biology' save_ save__citation.journal_id_ASTM _item_description.description ; The American Society for Testing and Materials (ASTM) code assigned to the journal cited (also referred to as the CODEN designator of the Chemical Abstracts Service); relevant for journal articles. ; _item.name '_citation.journal_id_ASTM' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_id_ASTM' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.journal_id_CSD _item_description.description ; The Cambridge Structural Database (CSD) code assigned to the journal cited; relevant for journal articles. This is also the system used at the Protein Data Bank (PDB). ; _item.name '_citation.journal_id_CSD' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_id_CSD' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case '0070' save_ save__citation.journal_id_ISSN _item_description.description ; The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles. ; _item.name '_citation.journal_id_ISSN' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_journal_id_ISSN' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line save_ save__citation.journal_volume _item_description.description ; Volume number of the journal cited; relevant for journal articles. ; _item.name '_citation.journal_volume' _item.category_id citation _item.mandatory_code no _pdbx_item_description.name "_citation.journal_volume" _pdbx_item_description.description "The volume number of the journal in which the article appeared. Example: 317" _item_aliases.alias_name '_citation_journal_volume' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _item_examples.case '174' save_ save__citation.page_first _item_description.description ; The first page of the citation; relevant for journal articles, books and book chapters. ; _item.name '_citation.page_first' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_page_first' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _pdbx_item_description.name "_citation.page_first" _pdbx_item_description.description "The starting page number of this article." save_ save__citation.page_last _item_description.description ; The last page of the citation; relevant for journal articles, books and book chapters. ; _item.name '_citation.page_last' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_page_last' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line _pdbx_item_description.name "_citation.page_last" _pdbx_item_description.description "The last page number of this article." save_ save__citation.pdbx_database_id_DOI _item_description.description ; Document Object Identifier used by doi.org to uniquely specify bibliographic entry. ; _item.name '_citation.pdbx_database_id_DOI' _item.category_id citation _item.mandatory_code no _item_type.code code _pdbx_item_type.name '_citation.pdbx_database_id_DOI' _pdbx_item_type.code citation_doi _item_examples.case '10.2345/S1384107697000225' _pdbx_item_description.name "_citation.pdbx_database_id_DOI" _pdbx_item_description.description "The document Object Identifier used by doi.org to uniquely specify bibliographic entry" _item_aliases.alias_name '_citation.rcsb_database_id_DOI' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__citation.pdbx_database_id_PubMed _item_description.description ; Ascession number used by PubMed to categorize a specific bibliographic entry. ; _item.name '_citation.pdbx_database_id_PubMed' _item.category_id citation _item.mandatory_code no _pdbx_item_description.name "_citation.pdbx_database_id_PubMed" _pdbx_item_description.description "The accession number used by PubMed to categorize a specific bibliographic entry" loop_ _item_range.maximum _item_range.minimum . -1 -1 -1 _item_type.code int _item_examples.case 12627512 _item_aliases.alias_name '_citation.rcsb_database_id_PubMed' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__citation.title _item_description.description ; The title of the citation; relevant for journal articles, books and book chapters. ; _item.name '_citation.title' _item.category_id citation _item.mandatory_code no _pdbx_item.name "_citation.title" _pdbx_item.mandatory_code yes _item_aliases.alias_name '_citation_title' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code text _pdbx_item_description.name "_citation.title" _pdbx_item_description.description "Title of the article or chapter or part of a book. This should be marked NULL if the author(s) listed wrote the entire book (or other work) and no sub-section of the book is being cited. Example: The Structure of Crystalline Profilin-Beta-Actin" _item_examples.case "Highly accurate protein structure prediction with AlphaFold" save_ save__citation.year _item_description.description ; The year of the citation; relevant for journal articles, books and book chapters. ; _item.name '_citation.year' _item.category_id citation _item.mandatory_code no _item_aliases.alias_name '_citation_year' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int _item_examples.case 1984 _pdbx_item_description.name "_citation.year" _pdbx_item_description.description "The year of publication of the article. Example: 2002" save_ ##################### ## CITATION_AUTHOR ## ##################### save_citation_author _category.description ; Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list. ; _category.id citation_author _category.mandatory_code no loop_ _category_key.name '_citation_author.citation_id' '_citation_author.ordinal' '_citation_author.name' loop_ _category_group.id 'inclusive_group' 'citation_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; loop_ _citation_author.citation_id _citation_author.ordinal _citation_author.name 1 "Jumper, John" 1 1 "Evans, Richard" 2 1 "Pritzel, Alexander" 3 1 "Green, Tim" 4 1 "Figurnov, Michael" 5 1 "Ronneberger, Olaf" 6 1 "Tunyasuvunakool, Kathryn" 7 1 "Bates, Russ" 8 1 "Zidek, Augustin" 9 1 "Potapenko, Anna" 10 1 "Bridgland, Alex" 11 1 "Meyer, Clemens" 12 1 "Kohl, Simon A. A." 13 1 "Ballard, Andrew J." 14 1 "Cowie, Andrew" 15 1 "Romera-Paredes, Bernardino" 16 1 "Nikolov, Stanislav" 17 1 "Jain, Rishub" 18 1 "Adler, Jonas" 19 1 "Back, Trevor" 20 1 "Petersen, Stig" 21 1 "Reiman, David" 22 1 "Clancy, Ellen" 23 1 "Zielinski, Michal" 24 1 "Steinegger, Martin" 25 1 "Pacholska, Michalina" 26 1 "Berghammer, Tamas" 27 1 "Silver, David" 28 1 "Vinyals, Oriol" 29 1 "Senior, Andrew W." 30 1 "Kavukcuoglu, Koray" 31 1 "Kohli, Pushmeet" 32 1 "Hassabis, Demis" 33 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__citation_author.citation_id _item_description.description ; This data item is a pointer to _citation.id in the CITATION category. ; _item.name '_citation_author.citation_id' _item.mandatory_code yes _item_aliases.alias_name '_citation_author_citation_id' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code save_ save__citation_author.name _item_description.description ; Name of an author of the citation; relevant for journal articles, books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). ; _item.name '_citation_author.name' _item.category_id citation_author _item.mandatory_code yes _item_aliases.alias_name '_citation_author_name' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code line loop_ _item_examples.case 'Bleary, Percival R.' "O'Neil, F.K." 'Van den Bossche, G.' 'Yang, D.-L.' 'Simonov, Yu.A' _pdbx_item.name "_citation_author.name" _pdbx_item.mandatory_code yes # _pdbx_item_description.name "_citation_author.name" _pdbx_item_description.description "Author of a journal article, book chapter, whole book, or thesis. It is not to be used for editor(s) names. Provide the authors' name by using surname (family, or last name), a comma, followed by period separated initials for first and middle names. The word Junior is abbreviated as Jr. Umlauts and other character modifiers should not be included." # _pdbx_item_examples.name "_citation_author.name" _pdbx_item_examples.case "Jones, T.J." _pdbx_item_examples.detail . # _pdbx_item_type.name "_citation_author.name" _pdbx_item_type.code author # save_ save__citation_author.ordinal _item_description.description ; This data item defines the order of the author's name in the list of authors of a citation. ; _item.name '_citation_author.ordinal' _item.category_id citation_author _item.mandatory_code yes _item_aliases.alias_name '_citation_author_ordinal' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code int save_ ################ ## DATABASE_2 ## ################ save_database_2 _category.description ; Data items in the DATABASE_2 category record details about the database identifiers of the data block. These data items are assigned by database managers and should only appear in a data block if they originate from that source. The name of this category, DATABASE_2, arose because the category name DATABASE was already in use in the core CIF dictionary, but was used differently from the way it needed to be used in the mmCIF dictionary. Since CIF data names cannot be changed once they have been adopted, a new category had to be created. ; _category.id database_2 _category.mandatory_code no loop_ _category_key.name '_database_2.database_id' '_database_2.database_code' loop_ _category_group.id 'inclusive_group' 'database_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _database_2.database_code AF-Q8W3K0-F1 _database_2.database_id AF ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__database_2.database_id _item_description.description ; An abbreviation that identifies the database. ; _item.name '_database_2.database_id' _item.category_id database_2 _item.mandatory_code yes _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail AF ; AlphaFold ; CAS ; Chemical Abstracts ; CSD ; Cambridge Structural Database (organic and metal-organic compounds) ; EMDB ; Electron Microscopy Data Bank ; ICSD ; Inorganic Crystal Structure Database ; MDF ; Metals Data File (metal structures) ; NDB ; Nucleic Acid Database ; NBS ; NBS (NIST) Crystal Data Database (lattice parameters) ; PDB ; Protein Data Bank ; PDF ; Powder Diffraction File (JCPDS/ICDD) ; RCSB ; Research Collaboratory for Structural Bioinformatics ; EBI ; European Bioinformatics Institute ; PDBE ; Protein Data Bank Europe ; BMRB ; Biological Magnetic Reference Data Bank ; WWPDB ; Worldwide Protein Data Bank ; PDB_ACC ; Protein Data Bank Versioned Accession ; save_ save__database_2.database_code _item_description.description ; The code assigned by the database identified in _database_2.database_id. ; _item.name '_database_2.database_code' _item.category_id database_2 _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 1ABC ABCDEF save_ ############ ## ENTITY ## ############ save_entity _category.description ; Data items in the ENTITY category record details (such as chemical composition, name and source) about the molecular entities that are present in the structure. Items in the various ENTITY subcategories provide a full chemical description of these molecular entities. Entities are of three types: polymer, non-polymer and water. Note that the water category includes only water; ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. The ENTITY category is specific to macromolecular CIF applications and replaces the function of the CHEMICAL category in the CIF core. It is important to remember that the ENTITY data are not the result of the crystallographic experiment; those results are represented by the ATOM_SITE data items. ENTITY data items describe the chemistry of the molecules under investigation and can most usefully be thought of as the ideal groups to which the structure is restrained or constrained during refinement. Entities are described only once, even in those structures that contain multiple observations of an entity. The STRUCT_ASYM data items, which reference the entity list, describe and label the contents of the asymmetric unit. ; _category.id entity _category.mandatory_code no _category_key.name '_entity.id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _entity.details ? _entity.formula_weight ? _entity.id 1 _entity.pdbx_description "Probable disease resistance protein At1g58602" _entity.pdbx_ec ? _entity.pdbx_fragment ? _entity.pdbx_mutation ? _entity.pdbx_number_of_molecules 1 _entity.src_method man _entity.type polymer ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity.details _item_description.description ; A description of special aspects of the entity. ; _item.name '_entity.details' _item.category_id entity _item.mandatory_code no _item_type.code text save_ save__entity.formula_weight _item_description.description ; Formula mass in Daltons of the entity. ; _item.name '_entity.formula_weight' _item.category_id entity _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 1.0 1.0 1.0 _item_type.code float save_ save__entity.id _item_description.description ; The value of _entity.id must uniquely identify a record in the ENTITY list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity.id' entity yes '_atom_site.label_entity_id' atom_site yes '_entity_poly.entity_id' entity_poly yes '_entity_poly_seq.entity_id' entity_poly_seq yes '_struct_asym.entity_id' struct_asym yes '_struct_ref.entity_id' struct_ref yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_entity_id' '_entity.id' '_entity_poly.entity_id' '_entity.id' '_entity_poly_seq.entity_id' '_entity_poly.entity_id' '_struct_asym.entity_id' '_entity.id' '_struct_ref.entity_id' '_entity.id' save_ save__entity.pdbx_description _item_description.description ; A description of the entity. Corresponds to the compound name in the PDB format. ; _item.name '_entity.pdbx_description' _item.category_id entity _item.mandatory_code no _pdbx_item.name "_entity.pdbx_description" _pdbx_item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'DNA (5'-D(*GP*(CH3)CP*GP*(CH3)CP*GP*C)-3')' PROFLAVINE 'PROTEIN (DEOXYRIBONUCLEASE I (E.C.3.1.21.1))' _item_aliases.alias_name '_entity.ndb_description' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 _pdbx_item_examples.name "_entity.pdbx_description" _pdbx_item_examples.case "Green fluorescent protein" _pdbx_item_examples.detail . save_ save__entity.pdbx_ec _item_description.description ; Enzyme Commission (EC) number(s) ; _item.name '_entity.pdbx_ec' _item.category_id entity _item.mandatory_code no _item_type.code ec-type _item_examples.case 2.7.7.7 _item_aliases.alias_name '_entity_keywords.ndb_ec' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity.pdbx_fragment _item_description.description ; Entity fragment description(s). ; _item.name '_entity.pdbx_fragment' _item.category_id entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'KLENOW FRAGMENT' 'REPLICASE OPERATOR HAIRPIN' 'C-TERMINAL DOMAIN' _item_aliases.alias_name '_entity_keywords.ndb_fragment' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity.pdbx_mutation _item_description.description ; Details about any entity mutation(s). ; _item.name '_entity.pdbx_mutation' _item.category_id entity _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Y31H' 'DEL(298-323)' _item_aliases.alias_name '_entity_keywords.ndb_mutation' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity.pdbx_number_of_molecules _item_description.description ; A place holder for the number of molecules of the entity in the entry. ; _item.name '_entity.pdbx_number_of_molecules' _item.category_id entity _item.mandatory_code no _item_type.code int loop_ _item_examples.case 1 2 3 _item_aliases.alias_name '_entity.ndb_number_of_molecules' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity.src_method _item_description.description ; The method by which the sample for the entity was produced. Entities isolated directly from natural sources (tissues, soil samples etc.) are expected to have further information in the ENTITY_SRC_NAT category. Entities isolated from genetically manipulated sources are expected to have further information in the ENTITY_SRC_GEN category. ; _item.name '_entity.src_method' _item.category_id entity _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail nat ; entity isolated from a natural source ; man ; entity isolated from a genetically manipulated source ; syn ; entity obtained synthetically ; _pdbx_item_description.name "_entity.src_method" _pdbx_item_description.description "The method by which the sample for the entity was produced" loop_ _pdbx_item_enumeration.name _pdbx_item_enumeration.value _pdbx_item_enumeration.detail "_entity.src_method" man . "_entity.src_method" nat . "_entity.src_method" syn . save_ save__entity.type _item_description.description ; Defines the type of the entity. Polymer entities are expected to have corresponding ENTITY_POLY and associated entries. Non-polymer entities are expected to have corresponding CHEM_COMP and associated entries. Water entities are not expected to have corresponding entries in the ENTITY category. ; _item.name '_entity.type' _item.category_id entity _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail polymer 'entity is a polymer' non-polymer 'entity is not a polymer' macrolide 'entity is a macrolide' water 'water in the solvent model' branched 'entity is branched' loop_ _pdbx_item_enumeration.name _pdbx_item_enumeration.value _pdbx_item_enumeration.detail "_entity.type" macrolide . "_entity.type" non-polymer . "_entity.type" polymer . "_entity.type" branched . "_entity.type" water . save_ ################# ## ENTITY_POLY ## ################# save_entity_poly _category.description ; Data items in the ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features. ; _category.id entity_poly _category.mandatory_code no _category_key.name '_entity_poly.entity_id' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _entity_poly.entity_id 1 _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;MAGELVSFAVNKLWDLLSHEYTLFQGVEDQVAELKSDLNLLKSFLKDADAKKHTSALVRYCVEEIKDIVYDAEDVLETFV QKEKLGTTSGIRKHIKRLTCIVPDRREIALYIGHVSKRITRVIRDMQSFGVQQMIVDDYMHPLRNREREIRRTFPKDNES GFVALEENVKKLVGYFVEEDNYQVVSITGMGGLGKTTLARQVFNHDMVTKKFDKLAWVSVSQDFTLKNVWQNILGDLKPK EEETKEEEKKILEMTEYTLQRELYQLLEMSKSLIVLDDIWKKEDWEVIKPIFPPTKGWKLLLTSRNESIVAPTNTKYFNF KPECLKTDDSWKLFQRIAFPINDASEFEIDEEMEKLGEKMIEHCGGLPLAIKVLGGMLAEKYTSHDWRRLSENIGSHLVG GRTNFNDDNNNSCNYVLSLSFEELPSYLKHCFLYLAHFPEDYEIKVENLSYYWAAEEIFQPRHYDGEIIRDVGDVYIEEL VRRNMVISERDVKTSRFETCHLHDMMREVCLLKAKEENFLQITSNPPSTANFQSTVTSRRLVYQYPTTLHVEKDINNPKL RSLVVVTLGSWNMAGSSFTRLELLRVLDLVQAKLKGGKLASCIGKLIHLRYLSLEYAEVTHIPYSLGNLKLLIYLNLHIS LSSRSNFVPNVLMGMQELRYLALPSLIERKTKLELSNLVKLETLENFSTKNSSLEDLRGMVRLRTLTIELIEETSLETLA ASIGGLKYLEKLEIDDLGSKMRTKEAGIVFDFVHLKRLRLELYMPRLSKEQHFPSHLTTLYLQHCRLEEDPMPILEKLLQ LKELELGHKSFSGKKMVCSSCGFPQLQKLSISGLKEWEDWKVEESSMPLLLTLNIFDCRKLKQLPDEHLPSHLTAISLKK CGLEDPIPTLERLVHLKELSLSELCGRIMVCTGGGFPQLHKLDLSELDGLEEWIVEDGSMPRLHTLEIRRCLKLKKLPNG FPQLQNLHLTEVEEWEEGMIVKQGSMPLLHTLYIWHCPKLPGEQHFPSHLTTVFLLGMYVEEDPMRILEKLLHLKNVSLF QSFSGKRMVCSGGGFPQLQKLSIREIEWEEWIVEQGSMPLLHTLYIGVCPNLKELPDGLRFIYSLKNLIVSKRWKKRLSE GGEDYYKVQHIPSVEFDD ; _entity_poly.pdbx_seq_one_letter_code_can ;MAGELVSFAVNKLWDLLSHEYTLFQGVEDQVAELKSDLNLLKSFLKDADAKKHTSALVRYCVEEIKDIVYDAEDVLETFV QKEKLGTTSGIRKHIKRLTCIVPDRREIALYIGHVSKRITRVIRDMQSFGVQQMIVDDYMHPLRNREREIRRTFPKDNES GFVALEENVKKLVGYFVEEDNYQVVSITGMGGLGKTTLARQVFNHDMVTKKFDKLAWVSVSQDFTLKNVWQNILGDLKPK EEETKEEEKKILEMTEYTLQRELYQLLEMSKSLIVLDDIWKKEDWEVIKPIFPPTKGWKLLLTSRNESIVAPTNTKYFNF KPECLKTDDSWKLFQRIAFPINDASEFEIDEEMEKLGEKMIEHCGGLPLAIKVLGGMLAEKYTSHDWRRLSENIGSHLVG GRTNFNDDNNNSCNYVLSLSFEELPSYLKHCFLYLAHFPEDYEIKVENLSYYWAAEEIFQPRHYDGEIIRDVGDVYIEEL VRRNMVISERDVKTSRFETCHLHDMMREVCLLKAKEENFLQITSNPPSTANFQSTVTSRRLVYQYPTTLHVEKDINNPKL RSLVVVTLGSWNMAGSSFTRLELLRVLDLVQAKLKGGKLASCIGKLIHLRYLSLEYAEVTHIPYSLGNLKLLIYLNLHIS LSSRSNFVPNVLMGMQELRYLALPSLIERKTKLELSNLVKLETLENFSTKNSSLEDLRGMVRLRTLTIELIEETSLETLA ASIGGLKYLEKLEIDDLGSKMRTKEAGIVFDFVHLKRLRLELYMPRLSKEQHFPSHLTTLYLQHCRLEEDPMPILEKLLQ LKELELGHKSFSGKKMVCSSCGFPQLQKLSISGLKEWEDWKVEESSMPLLLTLNIFDCRKLKQLPDEHLPSHLTAISLKK CGLEDPIPTLERLVHLKELSLSELCGRIMVCTGGGFPQLHKLDLSELDGLEEWIVEDGSMPRLHTLEIRRCLKLKKLPNG FPQLQNLHLTEVEEWEEGMIVKQGSMPLLHTLYIWHCPKLPGEQHFPSHLTTVFLLGMYVEEDPMRILEKLLHLKNVSLF QSFSGKRMVCSGGGFPQLQKLSIREIEWEEWIVEQGSMPLLHTLYIGVCPNLKELPDGLRFIYSLKNLIVSKRWKKRLSE GGEDYYKVQHIPSVEFDD ; _entity_poly.pdbx_strand_id A _entity_poly.type polypeptide(L) ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_poly.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_poly.entity_id' _item.category_id entity_poly _item.mandatory_code yes _item_type.code code save_ save__entity_poly.nstd_linkage _item_description.description ; A flag to indicate whether the polymer contains at least one monomer-to-monomer link different from that implied by _entity_poly.type. ; _item.name '_entity_poly.nstd_linkage' _item.category_id entity_poly _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'polymer contains no different links' n 'abbreviation for "no"' yes ; polymer contains at least one different link ; y 'abbreviation for "yes"' save_ save__entity_poly.nstd_monomer _item_description.description ; A flag to indicate whether the polymer contains at least one monomer that is not considered standard. ; _item.name '_entity_poly.nstd_monomer' _item.category_id entity_poly _item.mandatory_code no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'polymer contains no nonstandard monomers' n 'abbreviation for "no"' yes ; polymer contains at least one nonstandard monomer ; y 'abbreviation for "yes"' save_ save__entity_poly.pdbx_seq_one_letter_code _item_description.description ; Sequence of protein or nucleic acid polymer in standard one-letter codes of amino acids or nucleotides. Non-standard amino acids/nucleotides are represented by their Chemical Component Dictionary (CCD) codes in parenthesis. Deoxynucleotides are represented by the specially-assigned 2-letter CCD codes in parenthesis, with 'D' prefix added to their ribonucleotide counterparts. For hybrid polymer, each residue is represented by the code of its individual type. A cyclic polymer is represented in linear sequence from the chosen start to end. A for Alanine or Adenosine-5'-monophosphate C for Cysteine or Cytidine-5'-monophosphate D for Aspartic acid E for Glutamic acid F for Phenylalanine G for Glycine or Guanosine-5'-monophosphate H for Histidine I for Isoleucine or Inosinic Acid L for Leucine K for Lysine M for Methionine N for Asparagine or Unknown ribonucleotide O for Pyrrolysine P for Proline Q for Glutamine R for Arginine S for Serine T for Threonine U for Selenocysteine or Uridine-5'-monophosphate V for Valine W for Tryptophan Y for Tyrosine (DA) for 2'-deoxyadenosine-5'-monophosphate (DC) for 2'-deoxycytidine-5'-monophosphate (DG) for 2'-deoxyguanosine-5'-monophosphate (DT) for Thymidine-5'-monophosphate (MSE) for Selenomethionine (SEP) for Phosphoserine (PTO) for Phosphothreonine (PTR) for Phosphotyrosine (PCA) for Pyroglutamic acid (UNK) for Unknown amino acid (ACE) for Acetylation cap (NH2) for Amidation cap ; _item.name '_entity_poly.pdbx_seq_one_letter_code' _item.category_id entity_poly _item.mandatory_code no _item_type.code text _item_examples.case ; (MSE)SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD ; _pdbx_item.name "_entity_poly.pdbx_seq_one_letter_code" _pdbx_item.mandatory_code yes # _pdbx_item_description.name "_entity_poly.pdbx_seq_one_letter_code" _pdbx_item_description.description "Chemical sequence expressed as string of one-letter amino acid codes. Modifications and non-standard amino acids should be input using the three letter code in parenthesis, e.g. (MSE)" # _pdbx_item_examples.name "_entity_poly.pdbx_seq_one_letter_code" _pdbx_item_examples.case "HHHH(MSE)AKQRSG or AUCGGAAU" _pdbx_item_examples.detail . # _pdbx_item_type.name "_entity_poly.pdbx_seq_one_letter_code" _pdbx_item_type.code sequence_dep # _item_aliases.alias_name '_entity_poly.ndb_seq_one_letter_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_poly.pdbx_seq_one_letter_code_can _item_description.description ; Canonical sequence of protein or nucleic acid polymer in standard one-letter codes of amino acids or nucleotides, corresponding to the sequence in _entity_poly.pdbx_seq_one_letter_code. Non-standard amino acids/nucleotides are represented by the codes of their parents if parent is specified in _chem_comp.mon_nstd_parent_comp_id, or by letter 'X' if parent is not specified. Deoxynucleotides are represented by their canonical one-letter codes of A, C, G, or T. ; _item.name '_entity_poly.pdbx_seq_one_letter_code_can' _item.category_id entity_poly _item.mandatory_code no _item_type.code text _item_examples.case ; MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD ; _item_aliases.alias_name '_entity_poly.ndb_seq_one_letter_code_can' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_poly.pdbx_strand_id _item_description.description ; The PDB strand/chain id(s) corresponding to this polymer entity. ; _item.name '_entity_poly.pdbx_strand_id' _item.category_id entity_poly _item.mandatory_code no _item_type.code line loop_ _item_examples.case A B 'A,B,C' _pdbx_item_examples.name "_entity_poly.pdbx_strand_id" _pdbx_item_examples.case A,B _pdbx_item_examples.detail . _item_aliases.alias_name '_entity_poly.ndb_chain_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__entity_poly.type _item_description.description ; The type of the polymer. ; _item.name '_entity_poly.type' _item.category_id entity_poly _item.mandatory_code no _item_type.code line # _pdbx_item.name '_entity_poly.type' _pdbx_item.mandatory_code yes loop_ _item_enumeration.value 'polypeptide(D)' 'polypeptide(L)' 'polydeoxyribonucleotide' 'polyribonucleotide' 'polydeoxyribonucleotide/polyribonucleotide hybrid' 'cyclic-pseudo-peptide' 'peptide nucleic acid' 'other' loop_ _pdbx_item_enumeration.name _pdbx_item_enumeration.value _pdbx_item_enumeration.detail '_entity_poly.type' cyclic-pseudo-peptide . '_entity_poly.type' other . '_entity_poly.type' polydeoxyribonucleotide . '_entity_poly.type' 'polydeoxyribonucleotide/polyribonucleotide hybrid' . '_entity_poly.type' polypeptide(D) . '_entity_poly.type' polypeptide(L) . '_entity_poly.type' polyribonucleotide . save_ ##################### ## ENTITY_POLY_SEQ ## ##################### save_entity_poly_seq _category.description ; Data items in the ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity. ; _category.id entity_poly_seq _category.mandatory_code no loop_ _category_key.name '_entity_poly_seq.entity_id' '_entity_poly_seq.mon_id' '_entity_poly_seq.num' loop_ _category_group.id 'inclusive_group' 'entity_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; loop_ _entity_poly_seq.entity_id _entity_poly_seq.hetero _entity_poly_seq.mon_id _entity_poly_seq.num 1 n MET 1 1 n ALA 2 1 n GLY 3 1 n GLU 4 1 n LEU 5 1 n VAL 6 # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__entity_poly_seq.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_entity_poly_seq.entity_id' _item.category_id entity_poly_seq _item.mandatory_code yes _item_type.code code save_ save__entity_poly_seq.hetero _item_description.description ; A flag to indicate whether this monomer in the polymer is heterogeneous in sequence. ; _item.name '_entity_poly_seq.hetero' _item.category_id entity_poly_seq _item.mandatory_code no _item_default.value no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'sequence is not heterogeneous at this monomer' n 'abbreviation for "no"' yes 'sequence is heterogeneous at this monomer' y 'abbreviation for "yes"' save_ save__entity_poly_seq.mon_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_entity_poly_seq.mon_id' _item.category_id entity_poly_seq _item.mandatory_code yes _item_type.code ucode save_ save__entity_poly_seq.num _item_description.description ; The value of _entity_poly_seq.num must uniquely and sequentially identify a record in the ENTITY_POLY_SEQ list. Note that this item must be a number and that the sequence numbers must progress in increasing numerical order. ; loop_ _item.name _item.category_id _item.mandatory_code '_entity_poly_seq.num' entity_poly_seq yes '_atom_site.label_seq_id' atom_site yes '_struct_conf.beg_label_seq_id' struct_conf yes '_struct_conf.end_label_seq_id' struct_conf yes '_struct_ref_seq.seq_align_beg' struct_ref_seq yes '_struct_ref_seq.seq_align_end' struct_ref_seq yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_seq_id' '_entity_poly_seq.num' '_struct_conf.beg_label_seq_id' '_atom_site.label_seq_id' '_struct_conf.end_label_seq_id' '_atom_site.label_seq_id' '_struct_ref_seq.seq_align_beg' '_entity_poly_seq.num' '_struct_ref_seq.seq_align_end' '_entity_poly_seq.num' loop_ _item_range.maximum _item_range.minimum . 1 1 1 _item_type.code int save_ ############################## # PDBX_AUDIT_REVISION_DETAILS ############################## save_pdbx_audit_revision_details _category.description ; Data items in the PDBX_audit_revision_details category record descriptions of changes associated with PDBX_AUDIT_REVISION_HISTORY records. ; _category.id pdbx_audit_revision_details _category.mandatory_code no loop_ _category_key.name '_pdbx_audit_revision_details.data_content_type' '_pdbx_audit_revision_details.ordinal' '_pdbx_audit_revision_details.revision_ordinal' loop_ _category_group.id 'inclusive_group' 'audit_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _pdbx_audit_revision_details.data_content_type "Structure model" _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.type "Initial release" ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CHEM_COMP_INT _pdbx_category_context.category_id pdbx_audit_revision_details save_ save__pdbx_audit_revision_details.data_content_type _item_description.description ; The type of file that the pdbx_audit_revision_history record refers to. ; _item.name '_pdbx_audit_revision_details.data_content_type' _item.category_id pdbx_audit_revision_details _item.mandatory_code yes _item_type.code line _item_examples.case 'Structure model' loop_ _item_enumeration.value _item_enumeration.detail 'Structure model' 'Coordinate model file' 'NMR restraints' 'NMR restraints file' 'NMR shifts' 'NMR chemical shifts file' 'Structure factors' 'Diffraction structure factors file' 'Chemical component' 'Chemical component definition file' _item_linked.child_name '_pdbx_audit_revision_details.data_content_type' _item_linked.parent_name '_pdbx_audit_revision_history.data_content_type' save_ save__pdbx_audit_revision_details.description _item_description.description ; Additional details describing the revision. ; _item.name '_pdbx_audit_revision_details.description' _item.category_id pdbx_audit_revision_details _item.mandatory_code no _item_type.code text save_ save__pdbx_audit_revision_details.ordinal _item_description.description ; A unique identifier for the pdbx_audit_revision_details record. ; _item.name '_pdbx_audit_revision_details.ordinal' _item.category_id pdbx_audit_revision_details _item.mandatory_code yes _item_type.code int _item_examples.case 1 save_ save__pdbx_audit_revision_details.provider _item_description.description ; The provider of the revision. ; _item.name '_pdbx_audit_revision_details.provider' _item.category_id pdbx_audit_revision_details _item.mandatory_code no _pdbx_item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value 'repository' 'author' loop_ _item_examples.case 'repository' save_ save__pdbx_audit_revision_details.revision_ordinal _item_description.description ; A pointer to _pdbx_audit_revision_history.ordinal ; _item.name '_pdbx_audit_revision_details.revision_ordinal' _item.category_id pdbx_audit_revision_details _item.mandatory_code yes _item_type.code int _item_examples.case 1 _item_linked.child_name '_pdbx_audit_revision_details.revision_ordinal' _item_linked.parent_name '_pdbx_audit_revision_history.ordinal' save_ save__pdbx_audit_revision_details.type _item_description.description ; A type classification of the revision ; _item.name '_pdbx_audit_revision_details.type' _item.category_id pdbx_audit_revision_details _item.mandatory_code no _pdbx_item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value 'Initial release' 'Coordinate replacement' 'Obsolete' 'Remediation' loop_ _item_examples.case 'Initial release' save_ ############################## # PDBX_AUDIT_REVISION_HISTORY ############################## save_pdbx_audit_revision_history _category.description ; Data items in the PDBX_AUDIT_REVISION_HISTORY category record the revision history for a data entry. ; _category.id pdbx_audit_revision_history _category.mandatory_code no loop_ _category_key.name '_pdbx_audit_revision_history.data_content_type' '_pdbx_audit_revision_history.ordinal' loop_ _category_group.id 'inclusive_group' 'audit_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _pdbx_audit_revision_history.data_content_type "Structure model" _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.revision_date 2021-07-01 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CHEM_COMP_INT _pdbx_category_context.category_id pdbx_audit_revision_history save_ save__pdbx_audit_revision_history.data_content_type _item_description.description ; The type of file that the pdbx_audit_revision_history record refers to. ; _item.name '_pdbx_audit_revision_history.data_content_type' _item.category_id pdbx_audit_revision_history _item.mandatory_code yes _item_type.code line _item_examples.case 'Structure model' loop_ _item_enumeration.value _item_enumeration.detail 'Structure model' 'Coordinate model file' 'NMR restraints' 'NMR restraints file' 'NMR shifts' 'NMR chemical shifts file' 'Structure factors' 'Diffraction structure factors file' 'Chemical component' 'Chemical component definition file' save_ save__pdbx_audit_revision_history.major_revision _item_description.description ; The major version number of deposition release. ; _item.name '_pdbx_audit_revision_history.major_revision' _item.category_id pdbx_audit_revision_history _item.mandatory_code yes _item_type.code int _item_examples.case 1 save_ save__pdbx_audit_revision_history.minor_revision _item_description.description ; The minor version number of deposition release. ; _item.name '_pdbx_audit_revision_history.minor_revision' _item.category_id pdbx_audit_revision_history _item.mandatory_code yes _item_type.code int _item_examples.case 1 save_ save__pdbx_audit_revision_history.ordinal _item_description.description ; A unique identifier for the pdbx_audit_revision_history record. ; _item.name '_pdbx_audit_revision_history.ordinal' _item.category_id pdbx_audit_revision_history _item.mandatory_code yes _item_type.code int _item_examples.case 1 save_ save__pdbx_audit_revision_history.revision_date _item_description.description ; The release date of the revision ; _item.name '_pdbx_audit_revision_history.revision_date' _item.category_id pdbx_audit_revision_history _item.mandatory_code yes _item_type.code yyyy-mm-dd _item_examples.case 2017-03-08 save_ ######################## # PDBX_DATABASE_STATUS # ######################## save_pdbx_database_status _category.description ; These are internal records to keep track of data processing and status of the entry. ; _category.id 'pdbx_database_status' _category.mandatory_code no _category_key.name '_pdbx_database_status.entry_id' loop_ _category_group.id 'inclusive_group' 'database_group' 'pdbx_group' _category_examples.case ; _pdbx_database_status.entry_id AF-Q8W3K0-F1 _pdbx_database_status.recvd_initial_deposition_date 2021-07-01 _pdbx_database_status.status_code REL ; save_ save__pdbx_database_status.entry_id _item_description.description ; The value of _pdbx_database_status.entry_id identifies the data block. ; _item.name '_pdbx_database_status.entry_id' _item.category_id pdbx_database_status _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_database_status.entry_id' _item_linked.parent_name '_entry.id' _item_examples.case 'BDL001' _item_aliases.alias_name '_ndb_database_status.entry_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.recvd_initial_deposition_date _item_description.description ; The date of initial deposition. (The first message for deposition has been received.) ; _item.name '_pdbx_database_status.recvd_initial_deposition_date' _item.category_id pdbx_database_status _item.mandatory_code no _item_type.code yyyy-mm-dd _item_examples.case 1983-02-21 _item_aliases.alias_name '_ndb_database_status.recvd_initial_deposition_date' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_database_status.status_code _item_description.description ; Code for status of file. ; _item.name '_pdbx_database_status.status_code' _item.category_id pdbx_database_status _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail PROC 'To be processed' WAIT 'Processing started, waiting for author input to continue processing' REL 'Released' HOLD 'On hold until yyyy-mm-dd' HPUB 'On hold until publication' REFI 'Re-refined entry' OBS 'Entry has been obsoleted and replaced by another entry' WDRN 'Deposition has been withdrawn' AUTH 'Processed, waiting for author review and approval' POLC 'Processing, waiting for a policy decision' REPL 'Author sent new coordinates to be incorporated' AUCO 'Author corrections pending review' TRSF 'Entry transferred to another data repository' RMVD 'Entry has been removed' DEL 'Deprecated code' REV 'Deprecated code' UPD 'Deprecated code' BIB 'Deprecated code' loop_ _pdbx_item_enumeration.name _pdbx_item_enumeration.value _pdbx_item_enumeration.detail "_pdbx_database_status.status_code" AUTH . "_pdbx_database_status.status_code" HOLD . "_pdbx_database_status.status_code" HPUB . "_pdbx_database_status.status_code" OBS . "_pdbx_database_status.status_code" POLC . "_pdbx_database_status.status_code" PROC . "_pdbx_database_status.status_code" REFI . "_pdbx_database_status.status_code" REL . "_pdbx_database_status.status_code" REPL . "_pdbx_database_status.status_code" RMVD . "_pdbx_database_status.status_code" WAIT . "_pdbx_database_status.status_code" WDRN . loop_ _item_examples.case REL HPUB _item_aliases.alias_name '_ndb_database_status.status_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ######################## # PDBX_POLY_SEQ_SCHEME # ######################## save_pdbx_poly_seq_scheme _category.description ; The PDBX_POLY_SEQ_SCHEME category provides residue level nomenclature mapping for polymer entities. ; _category.id pdbx_poly_seq_scheme _category.mandatory_code no loop_ _category_key.name '_pdbx_poly_seq_scheme.asym_id' '_pdbx_poly_seq_scheme.entity_id' '_pdbx_poly_seq_scheme.mon_id' '_pdbx_poly_seq_scheme.seq_id' loop_ _category_group.id 'inclusive_group' 'struct_group' 'pdbx_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.hetero _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.seq_id A 1 1 n MET . A 1 A 2 1 n ALA . A 2 A 3 1 n GLY . A 3 A 4 1 n GLU . A 4 A 5 1 n LEU . A 5 A 6 1 n VAL . A 6 # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__pdbx_poly_seq_scheme.asym_id _item_description.description ; Pointer to _atom_site.label_asym_id. ; _item.name '_pdbx_poly_seq_scheme.asym_id' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_poly_seq_scheme.asym_id' _item_linked.parent_name '_struct_asym.id' loop_ _item_examples.case '1' 'A' '2B3' _item_aliases.alias_name '_ndb_poly_seq_scheme.id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.auth_seq_num _item_description.description ; Author provided residue number. This value may differ from the PDB residue number and may not correspond to residue numbering within the coordinate records. ; _item.name '_pdbx_poly_seq_scheme.auth_seq_num' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_poly_seq_scheme.auth_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.entity_id _item_description.description ; Pointer to _entity.id. ; _item.name '_pdbx_poly_seq_scheme.entity_id' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code yes _item_type.code code _item_linked.child_name '_pdbx_poly_seq_scheme.entity_id' _item_linked.parent_name '_entity_poly_seq.entity_id' _item_aliases.alias_name '_ndb_poly_seq_scheme.entity_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.hetero _item_description.description ; Pointer to _entity_poly_seq.hetero ; _item.name '_pdbx_poly_seq_scheme.hetero' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code no _item_default.value no _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail no 'sequence is not heterogeneous at this monomer' n 'abbreviation for "no"' yes 'sequence is heterogeneous at this monomer' y 'abbreviation for "yes"' _item_aliases.alias_name '_ndb_poly_seq_scheme.hetero' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.mon_id _item_description.description ; Pointer to _entity_poly_seq.mon_id. ; _item.name '_pdbx_poly_seq_scheme.mon_id' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code yes _item_type.code ucode _item_linked.child_name '_pdbx_poly_seq_scheme.mon_id' _item_linked.parent_name '_entity_poly_seq.mon_id' _item_aliases.alias_name '_ndb_poly_seq_scheme.mon_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.pdb_ins_code _item_description.description ; PDB insertion code. ; _item.name '_pdbx_poly_seq_scheme.pdb_ins_code' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_poly_seq_scheme.pdb_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.pdb_strand_id _item_description.description ; PDB strand/chain id. ; _item.name '_pdbx_poly_seq_scheme.pdb_strand_id' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_poly_seq_scheme.pdb_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.seq_id _item_description.description ; Pointer to _entity_poly_seq.num ; _item.name '_pdbx_poly_seq_scheme.seq_id' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code yes _item_type.code int _item_linked.child_name '_pdbx_poly_seq_scheme.seq_id' _item_linked.parent_name '_entity_poly_seq.num' _item_aliases.alias_name '_ndb_poly_seq_scheme.seq_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__pdbx_poly_seq_scheme.pdb_seq_num _item_description.description ; PDB residue number. ; _item.name '_pdbx_poly_seq_scheme.pdb_seq_num' _item.category_id pdbx_poly_seq_scheme _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_ndb_poly_seq_scheme.pdb_num' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ############## ## SOFTWARE ## ############## save_software _category.description ; Data items in the SOFTWARE category record details about the software used in the structure analysis, which implies any software used in the generation of any data items associated with the structure determination and structure representation. ; _category.id software _category.mandatory_code no _category_key.name '_software.pdbx_ordinal' loop_ _category_group.id 'inclusive_group' 'computing_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; loop_ _software.classification _software.date _software.description _software.name _software.pdbx_ordinal _software.type _software.version other ? "Structure prediction" AlphaFold 1 package v2.0 other ? "Secondary structure" dssp 2 library 4 ; save_ # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save__software.classification _item_description.description ; The classification of the program according to its major function. ; _item.name '_software.classification' _item.category_id software _item.mandatory_code yes _pdbx_item.name "_software.classification" _pdbx_item.mandatory_code yes _item_type.code uline loop_ _pdbx_item_enumeration.name _pdbx_item_enumeration.value _pdbx_item_enumeration.detail "_software.classification" "other" . save_ save__software.date _item_description.description ; The date the software was released. ; _item.name '_software.date' _item.category_id software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 1991-10-01 1990-04-30 save_ save__software.description _item_description.description ; Description of the software. ; _item.name '_software.description' _item.category_id software _item.mandatory_code no _item_type.code line _item_examples.case 'Structure prediction' save_ save__software.name _item_description.description ; The name of the software. ; _item.name '_software.name' _item.category_id software _item.mandatory_code yes _item_type.code text _item_examples.case 'AlphaFold' _pdbx_item.name "_software.name" _pdbx_item.mandatory_code yes _pdbx_item_description.name "_software.name" _pdbx_item_description.description "Select the appropriate software used in the structure determination" loop_ _pdbx_item_enumeration.name _pdbx_item_enumeration.value _pdbx_item_enumeration.detail '_software.name' AlphaFold 'Structure prediction' '_software.name' dssp 'Secondary structure' save_ save__software.pdbx_ordinal _item_description.description ; An ordinal index for this category ; _item.name '_software.pdbx_ordinal' _item.category_id software _item.mandatory_code yes _item_type.code int loop_ _item_examples.case 1 2 save_ save__software.type _item_description.description ; The classification of the software according to the most common types. ; _item.name '_software.type' _item.category_id software _item.mandatory_code no _item_type.code uline loop_ _item_enumeration.value _item_enumeration.detail program ; individual program with limited functionality ; library ; used by a program at load time ; package ; collections of programs with multiple functionality ; filter ; filters input and output streams ; jiffy ; short, simple program ; other ; all other kinds of software ; save_ save__software.version _item_description.description ; The version of the software. ; _item.name '_software.version' _item.category_id software _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'v1.0' 'beta' '3.1-2' 'unknown' _pdbx_item_description.description "The version of the software" save_ ################# ## STRUCT_ASYM ## ################# save_struct_asym _category.description ; Data items in the STRUCT_ASYM category record details about the structural elements in the asymmetric unit. ; _category.id struct_asym _category.mandatory_code no _category_key.name '_struct_asym.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _struct_asym.entity_id 1 _struct_asym.id A ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_asym.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_struct_asym.entity_id' _item.category_id struct_asym _item.mandatory_code yes _item_type.code code save_ save__struct_asym.id _item_description.description ; The value of _struct_asym.id must uniquely identify a record in the STRUCT_ASYM list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_asym.id' struct_asym yes '_atom_site.label_asym_id' atom_site yes '_struct_conf.beg_label_asym_id' struct_conf yes '_struct_conf.end_label_asym_id' struct_conf yes loop_ _item_linked.child_name _item_linked.parent_name '_atom_site.label_asym_id' '_struct_asym.id' '_struct_conf.beg_label_asym_id' '_atom_site.label_asym_id' '_struct_conf.end_label_asym_id' '_atom_site.label_asym_id' _item_type.code code loop_ _item_examples.case '1' 'A' '2B3' save_ ################# ## STRUCT_CONF ## ################# save_struct_conf _category.description ; Data items in the STRUCT_CONF category record details about the backbone conformation of a segment of polymer. Data items in the STRUCT_CONF_TYPE category define the criteria used to identify the backbone conformations. ; _category.id struct_conf _category.mandatory_code no _category_key.name '_struct_conf.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; loop_ _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_seq_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_seq_id _struct_conf.conf_type_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_seq_id _struct_conf.end_label_asym_id _struct_conf.end_label_comp_id _struct_conf.end_label_seq_id _struct_conf.id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.pdbx_end_PDB_ins_code A ALA 0 A ALA 2 HELX_RH_AL_P A HIS 0 A HIS 19 HELX_RH_AL_P1 ? ? A GLU 0 A GLU 20 BEND A GLU 0 A GLU 20 BEND1 ? ? A TYR 0 A TYR 21 HELX_RH_3T_P A PHE 0 A PHE 24 HELX_RH_3T_P1 ? ? A GLN 0 A GLN 25 TURN_TY1_P A GLY 0 A GLY 26 TURN_TY1_P1 ? ? A GLU 0 A GLU 28 HELX_RH_AL_P A LYS 0 A LYS 51 HELX_RH_AL_P2 ? ? # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_conf.beg_auth_asym_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_auth_asym_id' _item.mandatory_code no save_ save__struct_conf.beg_auth_comp_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_auth_comp_id' _item.mandatory_code no save_ save__struct_conf.beg_auth_seq_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_auth_seq_id' _item.mandatory_code no save_ save__struct_conf.beg_label_asym_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_label_asym_id' _item.mandatory_code yes save_ save__struct_conf.beg_label_comp_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_label_comp_id' _item.mandatory_code yes _item_type.code ucode save_ save__struct_conf.beg_label_seq_id _item_description.description ; A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_conf.beg_label_seq_id' _item.mandatory_code yes save_ save__struct_conf.conf_type_id _item_description.description ; This data item is a pointer to _struct_conf_type.id in the STRUCT_CONF_TYPE category. ; _item.name '_struct_conf.conf_type_id' _item.mandatory_code yes save_ save__struct_conf.end_auth_asym_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_auth_asym_id' _item.mandatory_code no save_ save__struct_conf.end_auth_comp_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_auth_comp_id' _item.mandatory_code no save_ save__struct_conf.end_auth_seq_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_auth_seq_id' _item.mandatory_code no save_ save__struct_conf.end_label_asym_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_label_asym_id' _item.mandatory_code yes save_ save__struct_conf.end_label_comp_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_label_comp_id' _item.mandatory_code yes _item_type.code ucode save_ save__struct_conf.end_label_seq_id _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_struct_conf.end_label_seq_id' _item.mandatory_code yes save_ save__struct_conf.id _item_description.description ; The value of _struct_conf.id must uniquely identify a record in the STRUCT_CONF list. Note that this item need not be a number; it can be any unique identifier. ; _item.name '_struct_conf.id' _item.category_id struct_conf _item.mandatory_code yes _item_type.code code save_ save__struct_conf.pdbx_beg_PDB_ins_code _item_description.description ; A component of the identifier for the residue at which the conformation segment starts. ; _item.name '_struct_conf.pdbx_beg_PDB_ins_code' _item.category_id struct_conf _item.mandatory_code no _item_type.code code _item_linked.child_name '_struct_conf.pdbx_beg_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_struct_conf.ndb_beg_label_ins_code_pdb' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_conf.pdbx_end_PDB_ins_code _item_description.description ; A component of the identifier for the residue at which the conformation segment ends. ; _item.name '_struct_conf.pdbx_end_PDB_ins_code' _item.category_id struct_conf _item.mandatory_code no _item_linked.child_name '_struct_conf.pdbx_end_PDB_ins_code' _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code' _item_aliases.alias_name '_struct_conf.ndb_end_label_ins_code_pdb' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ ###################### ## STRUCT_CONF_TYPE ## ###################### save_struct_conf_type _category.description ; Data items in the STRUCT_CONF_TYPE category record details about the criteria used to identify backbone conformations of a segment of polymer. ; _category.id struct_conf_type _category.mandatory_code no _category_key.name '_struct_conf_type.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; loop_ _struct_conf_type.criteria _struct_conf_type.id DSSP HELX_RH_AL_P DSSP BEND DSSP HELX_RH_3T_P DSSP TURN_TY1_P DSSP HELX_LH_PP_P DSSP STRN ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_conf_type.criteria _item_description.description ; The criteria used to assign this conformation type. ; _item.name '_struct_conf_type.criteria' _item.category_id struct_conf_type _item.mandatory_code no _item_type.code text _item_examples.case 'DSSP' save_ save__struct_conf_type.id _item_description.description ; The descriptor that categorizes the type of the conformation of the backbone of the polymer (whether protein or nucleic acid). Explicit values for the torsion angles that define each conformation are not given here, but it is expected that the author would provide such information in either the _struct_conf_type.criteria or _struct_conf_type.reference data items, or both. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_conf_type.id' struct_conf_type yes '_struct_conf.conf_type_id' struct_conf yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_conf.conf_type_id' '_struct_conf_type.id' _item_type.code ucode loop_ _item_enumeration.value _item_enumeration.detail BEND ; region with high backbone curvature without specific hydrogen bonding, a bend at residue i occurs when the angle between C$\_alpha(i)-C_\alpha(i-2) and C_\alpha(i+2) - C_\alpha(i)$ is greater than 70 degrees (protein) ; HELX_P ; helix with handedness and type not specified (protein) ; HELX_OT_P ; helix with handedness and type that do not conform to an accepted category (protein) ; # HELX_RH_P ; right-handed helix with type not specified (protein) ; HELX_RH_OT_P ; right-handed helix with type that does not conform to an accepted category (protein) ; HELX_RH_AL_P 'right-handed alpha helix (protein)' HELX_RH_GA_P 'right-handed gamma helix (protein)' HELX_RH_OM_P 'right-handed omega helix (protein)' HELX_RH_PI_P 'right-handed pi helix (protein)' HELX_RH_27_P 'right-handed 2-7 helix (protein)' HELX_RH_3T_P 'right-handed 3-10 helix (protein)' HELX_RH_PP_P 'right-handed polyproline helix (protein)' # HELX_LH_P ; left-handed helix with type not specified (protein) ; HELX_LH_OT_P ; left-handed helix with type that does not conform to an accepted category (protein) ; HELX_LH_AL_P 'left-handed alpha helix (protein)' HELX_LH_GA_P 'left-handed gamma helix (protein)' HELX_LH_OM_P 'left-handed omega helix (protein)' HELX_LH_PI_P 'left-handed pi helix (protein)' HELX_LH_27_P 'left-handed 2-7 helix (protein)' HELX_LH_3T_P 'left-handed 3-10 helix (protein)' HELX_LH_PP_P 'left-handed polyproline helix (protein)' # HELX_N ; helix with handedness and type not specified (nucleic acid) ; HELX_OT_N ; helix with handedness and type that do not conform to an accepted category (nucleic acid) ; # HELX_RH_N ; right-handed helix with type not specified (nucleic acid) ; HELX_RH_OT_N ; right-handed helix with type that does not conform to an accepted category (nucleic acid) ; HELX_RH_A_N 'right-handed A helix (nucleic acid)' HELX_RH_B_N 'right-handed B helix (nucleic acid)' HELX_RH_Z_N 'right-handed Z helix (nucleic acid)' # HELX_LH_N ; left-handed helix with type not specified (nucleic acid) ; HELX_LH_OT_N ; left-handed helix with type that does not conform to an accepted category (nucleic acid) ; HELX_LH_A_N 'left-handed A helix (nucleic acid)' HELX_LH_B_N 'left-handed B helix (nucleic acid)' HELX_LH_Z_N 'left-handed Z helix (nucleic acid)' # TURN_P 'turn with type not specified (protein)' TURN_OT_P ; turn with type that does not conform to an accepted category (protein) ; TURN_TY1_P 'type I turn (protein)' TURN_TY1P_P 'type I prime turn (protein)' TURN_TY2_P 'type II turn (protein)' TURN_TY2P_P 'type II prime turn (protein)' TURN_TY3_P 'type III turn (protein)' TURN_TY3P_P 'type III prime turn (protein)' # STRN 'beta strand (protein)' OTHER 'secondary structure type that does not conform to an accepted category, random coil (protein)' save_ ################ ## STRUCT_REF ## ################ save_struct_ref _category.description ; Data items in the STRUCT_REF category allow the author of a data block to relate the entities or biological units described in the data block to information archived in external databases. For references to the sequence of a polymer, the value of the data item _struct_ref.seq_align is used to indicate whether the correspondence between the sequence of the entity or biological unit in the data block and the sequence in the referenced database entry is 'complete' or 'partial'. If this value is 'partial', the region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. Similarly, the value of _struct_ref.seq_dif is used to indicate whether the two sequences contain point differences. If the value is 'yes', the differences may be identified and annotated using data items in the STRUCT_REF_SEQ_DIF category. ; _category.id struct_ref _category.mandatory_code no _category_key.name '_struct_ref.id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _struct_ref.db_code DRL9_ARATH _struct_ref.db_name UNP _struct_ref.entity_id 1 _struct_ref.id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_accession Q8W3K0 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ;MAGELVSFAVNKLWDLLSHEYTLFQGVEDQVAELKSDLNLLKSFLKDADAKKHTSALVRYCVEEIKDIVYDAEDVLETFV QKEKLGTTSGIRKHIKRLTCIVPDRREIALYIGHVSKRITRVIRDMQSFGVQQMIVDDYMHPLRNREREIRRTFPKDNES GFVALEENVKKLVGYFVEEDNYQVVSITGMGGLGKTTLARQVFNHDMVTKKFDKLAWVSVSQDFTLKNVWQNILGDLKPK EEETKEEEKKILEMTEYTLQRELYQLLEMSKSLIVLDDIWKKEDWEVIKPIFPPTKGWKLLLTSRNESIVAPTNTKYFNF KPECLKTDDSWKLFQRIAFPINDASEFEIDEEMEKLGEKMIEHCGGLPLAIKVLGGMLAEKYTSHDWRRLSENIGSHLVG GRTNFNDDNNNSCNYVLSLSFEELPSYLKHCFLYLAHFPEDYEIKVENLSYYWAAEEIFQPRHYDGEIIRDVGDVYIEEL VRRNMVISERDVKTSRFETCHLHDMMREVCLLKAKEENFLQITSNPPSTANFQSTVTSRRLVYQYPTTLHVEKDINNPKL RSLVVVTLGSWNMAGSSFTRLELLRVLDLVQAKLKGGKLASCIGKLIHLRYLSLEYAEVTHIPYSLGNLKLLIYLNLHIS LSSRSNFVPNVLMGMQELRYLALPSLIERKTKLELSNLVKLETLENFSTKNSSLEDLRGMVRLRTLTIELIEETSLETLA ASIGGLKYLEKLEIDDLGSKMRTKEAGIVFDFVHLKRLRLELYMPRLSKEQHFPSHLTTLYLQHCRLEEDPMPILEKLLQ LKELELGHKSFSGKKMVCSSCGFPQLQKLSISGLKEWEDWKVEESSMPLLLTLNIFDCRKLKQLPDEHLPSHLTAISLKK CGLEDPIPTLERLVHLKELSLSELCGRIMVCTGGGFPQLHKLDLSELDGLEEWIVEDGSMPRLHTLEIRRCLKLKKLPNG FPQLQNLHLTEVEEWEEGMIVKQGSMPLLHTLYIWHCPKLPGEQHFPSHLTTVFLLGMYVEEDPMRILEKLLHLKNVSLF QSFSGKRMVCSGGGFPQLQKLSIREIEWEEWIVEQGSMPLLHTLYIGVCPNLKELPDGLRFIYSLKNLIVSKRWKKRLSE GGEDYYKVQHIPSVEFDD ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ref.db_code _item_description.description ; The code for this entity or biological unit or for a closely related entity or biological unit in the named database. ; _item.name '_struct_ref.db_code' _item.category_id struct_ref _item.mandatory_code yes _item_type.code line loop_ _item_examples.case '1ABC' 'ABCDEF' save_ save__struct_ref.db_name _item_description.description ; The name of the database containing reference information about this entity or biological unit. ; _item.name '_struct_ref.db_name' _item.category_id struct_ref _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'PDB' 'CSD' 'Genbank' 'UNP' _pdbx_item_description.name "_struct_ref.db_name" _pdbx_item_description.description "The name of the database from which the sequence reference is derived" save_ save__struct_ref.entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_struct_ref.entity_id' _item.mandatory_code yes _pdbx_item_description.name "_struct_ref.entity_id" _pdbx_item_description.description "The numerical identifier of a unique polymeric sequence within the entry" save_ save__struct_ref.id _item_description.description ; The value of _struct_ref.id must uniquely identify a record in the STRUCT_REF list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ref.id' struct_ref yes '_struct_ref_seq.ref_id' struct_ref_seq yes loop_ _item_linked.child_name _item_linked.parent_name '_struct_ref_seq.ref_id' '_struct_ref.id' _item_type.code code save_ save__struct_ref.pdbx_align_begin _item_description.description ; Beginning index in the chemical sequence from the reference database. ; _item.name '_struct_ref.pdbx_align_begin' _item.category_id struct_ref _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref.rcsb_align_begin' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref.pdbx_align_end _item_description.description ; Ending index in the chemical sequence from the reference database. ; _item.name '_struct_ref.pdbx_align_end' _item.category_id struct_ref _item.mandatory_code no _item_type.code code loop_ _item_examples.case '105' '245' save_ save__struct_ref.pdbx_db_accession _item_description.description ; Accession code assigned by the reference database. ; _item.name '_struct_ref.pdbx_db_accession' _item.category_id struct_ref _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'Q8W3K0' _pdbx_item_description.name "_struct_ref.pdbx_db_accession" _pdbx_item_description.description "The accession code of the database sequence reference" # _item_aliases.alias_name '_struct_ref.rcsb_db_accession' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref.pdbx_db_isoform _item_description.description ; Database code assigned by the reference database for a sequence isoform. An isoform sequence is an alternative protein sequence that can be generated from the same gene by a single or by a combination of biological events such as: alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting. ; _item.name '_struct_ref.pdbx_db_isoform' _item.category_id struct_ref _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'P29994-6' save_ save__struct_ref.pdbx_seq_one_letter_code _item_description.description ; Database chemical sequence expressed as string of one-letter amino acid codes. ; _item.name '_struct_ref.pdbx_seq_one_letter_code' _item.category_id struct_ref _item.mandatory_code no _item_type.code text _item_examples.case ; A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil O for water X for other ; _item_aliases.alias_name '_struct_ref.rcsb_seq_one_letter_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ #################### ## STRUCT_REF_SEQ ## #################### save_struct_ref_seq _category.description ; Data items in the STRUCT_REF_SEQ category provide a mechanism for indicating and annotating a region (or regions) of alignment between the sequence of an entity or biological unit described in the data block and the sequence in the referenced database entry. ; _category.id struct_ref_seq _category.mandatory_code no _category_key.name '_struct_ref_seq.align_id' loop_ _category_group.id 'inclusive_group' 'struct_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _struct_ref_seq.align_id 1 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.db_align_end 1138 _struct_ref_seq.pdbx_PDB_id_code AF-Q8W3K0-F1 _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 1138 _struct_ref_seq.pdbx_db_accession Q8W3K0 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.ref_id 1 _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.seq_align_end 1138 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__struct_ref_seq.align_id _item_description.description ; The value of _struct_ref_seq.align_id must uniquely identify a record in the STRUCT_REF_SEQ list. Note that this item need not be a number; it can be any unique identifier. ; loop_ _item.name _item.category_id _item.mandatory_code '_struct_ref_seq.align_id' struct_ref_seq yes _item_type.code code save_ save__struct_ref_seq.db_align_beg _item_description.description ; The sequence position in the referenced database entry at which the alignment begins. ; _item.name '_struct_ref_seq.db_align_beg' _item.mandatory_code yes _item_type.code int save_ save__struct_ref_seq.db_align_end _item_description.description ; The sequence position in the referenced database entry at which the alignment ends. ; _item.name '_struct_ref_seq.db_align_end' _item.mandatory_code yes _item_type.code int save_ save__struct_ref_seq.pdbx_PDB_id_code _item_description.description ; The PDB code of the structure. ; _item.name '_struct_ref_seq.pdbx_PDB_id_code' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code _item_examples.case 'AF-Q8W3K0-F1' _item_aliases.alias_name '_struct_ref_seq.ndb_pdb_id_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq.pdbx_auth_seq_align_beg _item_description.description ; Initial position in the PDB sequence segment. ; _item.name '_struct_ref_seq.pdbx_auth_seq_align_beg' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref_seq.ndb_auth_seq_align_beg' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 _item_linked.child_name '_struct_ref_seq.pdbx_auth_seq_align_beg' _item_linked.parent_name '_pdbx_poly_seq_scheme.pdb_seq_num' save_ save__struct_ref_seq.pdbx_auth_seq_align_end _item_description.description ; Ending position in the PDB sequence segment ; _item.name '_struct_ref_seq.pdbx_auth_seq_align_end' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref_seq.ndb_auth_seq_align_end' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 _item_linked.child_name '_struct_ref_seq.pdbx_auth_seq_align_end' _item_linked.parent_name '_pdbx_poly_seq_scheme.pdb_seq_num' save_ save__struct_ref_seq.pdbx_db_accession _item_description.description ; Accession code of the reference database. ; _item.name '_struct_ref_seq.pdbx_db_accession' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'Q8W3K0' _item_aliases.alias_name '_struct_ref_seq.ndb_db_accession' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq.pdbx_db_align_beg_ins_code _item_description.description ; Initial insertion code of the sequence segment of the reference database. ; _item.name '_struct_ref_seq.pdbx_db_align_beg_ins_code' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref_seq.ndb_db_align_beg_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq.pdbx_db_align_end_ins_code _item_description.description ; Ending insertion code of the sequence segment of the reference database. ; _item.name '_struct_ref_seq.pdbx_db_align_end_ins_code' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref_seq.ndb_db_align_end_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__struct_ref_seq.pdbx_seq_align_beg_ins_code _item_description.description ; Initial insertion code of the PDB sequence segment. ; _item.name '_struct_ref_seq.pdbx_seq_align_beg_ins_code' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref_seq.ndb_seq_align_beg_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 _item_linked.child_name '_struct_ref_seq.pdbx_seq_align_beg_ins_code' _item_linked.parent_name '_pdbx_poly_seq_scheme.pdb_ins_code' save_ save__struct_ref_seq.pdbx_seq_align_end_ins_code _item_description.description ; Ending insertion code of the sequence segment ; _item.name '_struct_ref_seq.pdbx_seq_align_end_ins_code' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' _item_aliases.alias_name '_struct_ref_seq.ndb_seq_align_end_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 _item_linked.child_name '_struct_ref_seq.pdbx_seq_align_end_ins_code' _item_linked.parent_name '_pdbx_poly_seq_scheme.pdb_ins_code' save_ save__struct_ref_seq.pdbx_strand_id _item_description.description ; The PDB strand/chain ID . ; _item.name '_struct_ref_seq.pdbx_strand_id' _item.category_id struct_ref_seq _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'A' 'B' _item_aliases.alias_name '_struct_ref_seq.ndb_chain_id' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 # _item_linked.child_name '_struct_ref_seq.pdbx_strand_id' _item_linked.parent_name '_pdbx_poly_seq_scheme.pdb_strand_id' save_ save__struct_ref_seq.ref_id _item_description.description ; This data item is a pointer to _struct_ref.id in the STRUCT_REF category. ; _item.name '_struct_ref_seq.ref_id' _item.mandatory_code yes save_ save__struct_ref_seq.seq_align_beg _item_description.description ; The sequence position in the entity or biological unit described in the data block at which the alignment begins. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_struct_ref_seq.seq_align_beg' _item.mandatory_code yes save_ save__struct_ref_seq.seq_align_end _item_description.description ; The sequence position in the entity or biological unit described in the data block at which the alignment ends. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_struct_ref_seq.seq_align_end' _item.mandatory_code yes save_ ############### ## ATOM_SITE ## ############### save_atom_site _category.description ; Data items in the ATOM_SITE category record details about the atom sites in a macromolecular structure, including atom, residue, and sequuence identifiers and their positional coordinates. wwPDB recommends wwPDB-assigned residue number, residue ID, and chain ID, _atom_site.auth_seq_id _atom_site.auth_comp_id, and _atom_site.auth_asym_id, respectively, to be used for publication materials. ; _category.id atom_site _category.mandatory_code no _category_key.name '_atom_site.id' loop_ _category_group.id 'inclusive_group' 'atom_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num _atom_site.pdbx_sifts_xref_db_acc _atom_site.pdbx_sifts_xref_db_name _atom_site.pdbx_sifts_xref_db_num _atom_site.pdbx_sifts_xref_db_res ATOM 1 N N . MET A 1 1 ? -9.212 -5.798 33.490 1.0 63.75 ? 1 MET A N 1 Q8W3K0 UNP 1 M ATOM 2 C CA . MET A 1 1 ? -10.075 -6.130 32.322 1.0 63.75 ? 1 MET A CA 1 Q8W3K0 UNP 1 M ATOM 3 C C . MET A 1 1 ? -11.469 -6.615 32.714 1.0 63.75 ? 1 MET A C 1 Q8W3K0 UNP 1 M ATOM 4 C CB . MET A 1 1 ? -9.419 -7.112 31.341 1.0 63.75 ? 1 MET A CB 1 Q8W3K0 UNP 1 M ATOM 5 O O . MET A 1 1 ? -12.429 -6.075 32.184 1.0 63.75 ? 1 MET A O 1 Q8W3K0 UNP 1 M ATOM 6 C CG . MET A 1 1 ? -8.311 -6.411 30.547 1.0 63.75 ? 1 MET A CG 1 Q8W3K0 UNP 1 M ATOM 7 S SD . MET A 1 1 ? -7.766 -7.280 29.061 1.0 63.75 ? 1 MET A SD 1 Q8W3K0 UNP 1 M ATOM 8 C CE . MET A 1 1 ? -7.045 -8.751 29.798 1.0 63.75 ? 1 MET A CE 1 Q8W3K0 UNP 1 M ATOM 9 N N . ALA A 1 2 ? -11.624 -7.579 33.634 1.0 66.38 ? 2 ALA A N 1 Q8W3K0 UNP 2 A ATOM 10 C CA . ALA A 1 2 ? -12.951 -8.096 34.007 1.0 66.38 ? 2 ALA A CA 1 Q8W3K0 UNP 2 A ATOM 11 C C . ALA A 1 2 ? -13.898 -7.016 34.578 1.0 66.38 ? 2 ALA A C 1 Q8W3K0 UNP 2 A ATOM 12 C CB . ALA A 1 2 ? -12.757 -9.248 34.997 1.0 66.38 ? 2 ALA A CB 1 Q8W3K0 UNP 2 A ATOM 13 O O . ALA A 1 2 ? -15.076 -7.002 34.241 1.0 66.38 ? 2 ALA A O 1 Q8W3K0 UNP 2 A ATOM 14 N N . GLY A 1 3 ? -13.371 -6.075 35.376 1.0 65.17 ? 3 GLY A N 1 Q8W3K0 UNP 3 G ATOM 15 C CA . GLY A 1 3 ? -14.121 -4.919 35.893 1.0 65.17 ? 3 GLY A CA 1 Q8W3K0 UNP 3 G ATOM 16 C C . GLY A 1 3 ? -14.776 -4.060 34.807 1.0 65.17 ? 3 GLY A C 1 Q8W3K0 UNP 3 G ATOM 17 O O . GLY A 1 3 ? -15.957 -3.733 34.895 1.0 65.17 ? 3 GLY A O 1 Q8W3K0 UNP 3 G ATOM 18 N N . GLU A 1 4 ? -14.021 -3.740 33.758 1.0 65.58 ? 4 GLU A N 1 Q8W3K0 UNP 4 E # - - - - data truncated for brevity - - - - ; save_ save__atom_site.group_PDB _item_description.description ; The group of atoms to which the atom site belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. ; _item.name '_atom_site.group_PDB' _item.category_id atom_site _item.mandatory_code no _item_type.code code loop_ _item_enumeration.value ATOM HETATM save_ save__atom_site.id _item_description.description ; The value of _atom_site.id must uniquely identify a record in the ATOM_SITE list. Note that this item need not be a number; it can be any unique identifier. This data item was introduced to provide compatibility between small-molecule and macromolecular CIFs. In a small-molecule CIF, _atom_site_label is the identifier for the atom. In a macromolecular CIF, the atom identifier is the aggregate of _atom_site.label_alt_id, _atom_site.label_asym_id, _atom_site.label_atom_id, _atom_site.label_comp_id and _atom_site.label_seq_id. For the two types of files to be compatible, a formal identifier for the category had to be introduced that was independent of the different modes of identifying the atoms. For compatibility with older CIFs, _atom_site_label is aliased to _atom_site.id. In general, this aggregate identifier does not uniquely identify an atom site as for non-polymers _atom_site.label_seq_id is '.'. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.id' atom_site yes _item_aliases.alias_name '_atom_site_label' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code code loop_ _item_examples.case '5' 'C12' 'Ca3g28' 'Fe3+17' 'H*251' 'boron2a' 'C_a_phe_83_a_0' 'Zn_Zn_301_A_0' save_ save__atom_site.type_symbol _item_description.description ; This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category. ; _item.name '_atom_site.type_symbol' _item.category_id atom_site _item.mandatory_code yes _item_type.code code _item_aliases.alias_name '_atom_site_type_symbol' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 save_ save__atom_site.label_atom_id _item_description.description ; A component of the identifier for this atom site. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category. ; _item.name '_atom_site.label_atom_id' _item.mandatory_code yes _item_sub_category.id mm_atom_site_label _item_type.code atcode save_ save__atom_site.label_alt_id _item_description.description ; A place holder to indicate alternate conformation. The alternate conformation can be an entire polymer chain, or several residues or partial residue (several atoms within one residue). If an atom is provided in more than one position, then a non-blank alternate location indicator must be used for each of the atomic positions. ; _item.name '_atom_site.label_alt_id' _item.mandatory_code yes _item_sub_category.id mm_atom_site_label _item_type.code code save_ save__atom_site.label_comp_id _item_description.description ; A component of the identifier for this atom site. This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_atom_site.label_comp_id' _item.mandatory_code yes _item_sub_category.id mm_atom_site_label _item_type.code ucode save_ save__atom_site.label_asym_id _item_description.description ; A component of the identifier for this atom site. For further details, see the definition of the STRUCT_ASYM category. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category. ; _item.name '_atom_site.label_asym_id' _item.mandatory_code yes _item_sub_category.id mm_atom_site_label _item_type.code code _pdbx_item_description.name "_atom_site.label_asym_id" _pdbx_item_description.description "Enter chain ID of the ligand. Example: G" save_ save__atom_site.label_entity_id _item_description.description ; This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_atom_site.label_entity_id' _item.category_id atom_site _item.mandatory_code yes _item_type.code code save_ save__atom_site.label_seq_id _item_description.description ; This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category. ; _item.name '_atom_site.label_seq_id' _item.mandatory_code yes _item_type.code int _pdbx_item_description.name '_atom_site.label_seq_id' _pdbx_item_description.description 'Enter residue number of the ligand. Example: 1125' save_ save__atom_site.pdbx_PDB_ins_code _item_description.description ; PDB insertion code. ; _item.name '_atom_site.pdbx_PDB_ins_code' _item.category_id atom_site _item.mandatory_code no _item_type.code code _item_aliases.alias_name '_atom_site.ndb_ins_code' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 save_ save__atom_site.Cartn_x _item_description.description ; The x atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_atom_site.Cartn_x' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Cartn_x' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.Cartn_y' '_atom_site.Cartn_z' _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__atom_site.Cartn_y _item_description.description ; The y atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_atom_site.Cartn_y' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Cartn_y' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.Cartn_x' '_atom_site.Cartn_z' _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__atom_site.Cartn_z _item_description.description ; The z atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes. ; _item.name '_atom_site.Cartn_z' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_Cartn_z' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 loop_ _item_dependent.dependent_name '_atom_site.Cartn_x' '_atom_site.Cartn_y' _item_sub_category.id cartesian_coordinate _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__atom_site.occupancy _item_description.description ; The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not exceed 1.0 unless it is a dummy site. ; _item.name '_atom_site.occupancy' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_occupancy' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_default.value 1.0 _item_type.code float _item_type_conditions.code esd save_ save__atom_site.B_iso_or_equiv _item_description.description ; Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, B~eq~, calculated from the anisotropic displacement parameters. B~eq~ = (1/3) sum~i~[sum~j~(B^ij^ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths B^ij^ = 8 pi^2^ U^ij^ Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. Note - The particular type of ADP stored in this item is qualified by item _refine.pdbx_adp_type. ; _item.name '_atom_site.B_iso_or_equiv' _item.category_id atom_site _item.mandatory_code no _item_aliases.alias_name '_atom_site_B_iso_or_equiv' _item_aliases.dictionary cif_core.dic _item_aliases.version 2.0.1 _item_type.code float _item_type_conditions.code esd _item_units.code 8pi2_angstroms_squared save_ save__atom_site.pdbx_formal_charge _item_description.description ; The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. ; _item.name '_atom_site.pdbx_formal_charge' _item.category_id atom_site _item.mandatory_code no _item_default.value 0 loop_ _item_range.maximum _item_range.minimum 8 8 8 -8 -8 -8 _item_type.code int loop_ _item_examples.case _item_examples.detail 1 'for an ammonium nitrogen' -1 'for a chloride ion' save_ save__atom_site.auth_seq_id _item_description.description ; An alternative identifier for _atom_site.label_seq_id that may be provided by an author in order to match the identification used in the publication that describes the structure. Note that this is not necessarily a number, that the values do not have to be positive, and that the value does not have to correspond to the value of _atom_site.label_seq_id. The value of _atom_site.label_seq_id is required to be a sequential list of positive integers. The author may assign values to _atom_site.auth_seq_id in any desired way. For instance, the values may be used to relate this structure to a numbering scheme in a homologous structure, including sequence gaps or insertion codes. Alternatively, a scheme may be used for a truncated polymer that maintains the numbering scheme of the full length polymer. In all cases, the scheme used here must match the scheme used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_seq_id' atom_site no '_struct_conf.beg_auth_seq_id' struct_conf no '_struct_conf.end_auth_seq_id' struct_conf no loop_ _item_linked.child_name _item_linked.parent_name '_struct_conf.beg_auth_seq_id' '_atom_site.auth_seq_id' '_struct_conf.end_auth_seq_id' '_atom_site.auth_seq_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code code save_ save__atom_site.auth_comp_id _item_description.description ; An alternative identifier for _atom_site.label_comp_id that may be provided by an author in order to match the identification used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_comp_id' atom_site no '_struct_conf.beg_auth_comp_id' struct_conf no '_struct_conf.end_auth_comp_id' struct_conf no loop_ _item_linked.child_name _item_linked.parent_name '_struct_conf.beg_auth_comp_id' '_atom_site.auth_comp_id' '_struct_conf.end_auth_comp_id' '_atom_site.auth_comp_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code code save_ save__atom_site.auth_asym_id _item_description.description ; An alternative identifier for _atom_site.label_asym_id that may be provided by an author in order to match the identification used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_asym_id' atom_site yes '_struct_conf.beg_auth_asym_id' struct_conf no '_struct_conf.end_auth_asym_id' struct_conf no loop_ _item_linked.child_name _item_linked.parent_name '_struct_conf.beg_auth_asym_id' '_atom_site.auth_asym_id' '_struct_conf.end_auth_asym_id' '_atom_site.auth_asym_id' _item_sub_category.id mm_atom_site_auth_label _item_type.code code save_ save__atom_site.auth_atom_id _item_description.description ; An alternative identifier for _atom_site.label_atom_id that may be provided by an author in order to match the identification used in the publication that describes the structure. ; loop_ _item.name _item.category_id _item.mandatory_code '_atom_site.auth_atom_id' atom_site no _item_sub_category.id mm_atom_site_auth_label _item_type.code atcode save_ save__atom_site.pdbx_PDB_model_num _item_description.description ; PDB model number. ; _item.name '_atom_site.pdbx_PDB_model_num' _item.category_id atom_site _item.mandatory_code no _item_type.code int _item_aliases.alias_name '_atom_site.ndb_model' _item_aliases.dictionary 'cif_rcsb.dic' _item_aliases.version 1.1 _item_range.maximum . _item_range.minimum 0 save_ save__atom_site.pdbx_sifts_xref_db_acc _item_description.description ; The accession code related to the additional external database entry. ; _item.name '_atom_site.pdbx_sifts_xref_db_acc' _item.category_id atom_site _item.mandatory_code no _item_type.code code save_ save__atom_site.pdbx_sifts_xref_db_name _item_description.description ; The name of additional external databases with residue level mapping. ; _item.name '_atom_site.pdbx_sifts_xref_db_name' _item.category_id atom_site _item.mandatory_code no _item_type.code code save_ save__atom_site.pdbx_sifts_xref_db_num _item_description.description ; The sequence position of the external database entry that corresponds to the residue mapping defined by the SIFTS process. ; _item.name '_atom_site.pdbx_sifts_xref_db_num' _item.category_id atom_site _item.mandatory_code no _item_type.code code save_ save__atom_site.pdbx_sifts_xref_db_res _item_description.description ; Describes the residue type of the given UniProt match ; _item.name '_atom_site.pdbx_sifts_xref_db_res' _item.category_id atom_site _item.mandatory_code no _item_type.code ucode loop_ _item_examples.case _item_examples.detail A 'alanine' R 'arginine' N 'asparagine' D 'aspartic acid' C 'cysteine' Q 'glutamine' E 'glutamic acid' G 'glycine' H 'histidine' I 'isoleucine' L 'leucine' K 'lysine' M 'methionine' F 'phenylalanine' P 'proline' U 'selenocysteine' S 'serine' T 'threonine' W 'tryptophan' Y 'tyrosine' V 'valine' O 'pyrrolysine' X 'other' save_ ######################################################################## # # # MODELING EXTENSION DICTIONARY DERIVED CATEGORIES # # # ######################################################################## ############################## ## MA_TARGET_REF_DB_DETAILS ## ############################## save_ma_target_ref_db_details _category.description ; Data items in the MA_TARGET_REF_DB_DETAILS category record details about the reference databases for the target sequences. ; _category.id ma_target_ref_db_details _category.mandatory_code no loop_ _category_key.name '_ma_target_ref_db_details.target_entity_id' '_ma_target_ref_db_details.db_name' loop_ _category_group.id 'inclusive_group' 'ma_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _ma_target_ref_db_details.db_accession Q8W3K0 _ma_target_ref_db_details.db_code DRL9_ARATH _ma_target_ref_db_details.db_name UNP _ma_target_ref_db_details.ncbi_taxonomy_id 3702 _ma_target_ref_db_details.organism_scientific "Arabidopsis thaliana" _ma_target_ref_db_details.seq_db_align_begin 1 _ma_target_ref_db_details.seq_db_align_end 1138 _ma_target_ref_db_details.seq_db_isoform ? _ma_target_ref_db_details.target_entity_id 1 _ma_target_ref_db_details.gene_name At1g58602 _ma_target_ref_db_details.seq_db_sequence_checksum 13E94BE58A924207 _ma_target_ref_db_details.seq_db_sequence_version_date 2002-03-01 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ma_target_ref_db_details save_ save__ma_target_ref_db_details.db_accession _item_description.description ; Accession code assigned by the reference database. ; _item.name '_ma_target_ref_db_details.db_accession' _item.category_id ma_target_ref_db_details _item.mandatory_code yes _item_type.code code loop_ _item_examples.case 'P07617' '11612676' 'B2RHG4' save_ save__ma_target_ref_db_details.db_code _item_description.description ; The code for this entity or biological unit or for a closely related entity or biological unit in the named database. This can include the version number. ; _item.name '_ma_target_ref_db_details.db_code' _item.category_id ma_target_ref_db_details _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'B2RHG4_PORG3' 'AE000513.1' save_ save__ma_target_ref_db_details.db_name _item_description.description ; The name of the database containing reference information about this entity or biological unit. ; _item.name '_ma_target_ref_db_details.db_name' _item.category_id ma_target_ref_db_details _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail 'UNP' 'UniProtKB' 'GB' 'Genbank' 'OrthoDB' 'OrthoDB' 'NCBI' 'NCBI' 'JGI' 'JGI' 'Other' 'Other' save_ save__ma_target_ref_db_details.ncbi_taxonomy_id _item_description.description ; Taxonomy identifier provided by NCBI. ; _item.name '_ma_target_ref_db_details.ncbi_taxonomy_id' _item.category_id ma_target_ref_db_details _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1294385' save_ save__ma_target_ref_db_details.organism_scientific _item_description.description ; Scientific name of the organism. ; _item.name '_ma_target_ref_db_details.organism_scientific' _item.category_id ma_target_ref_db_details _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'Saccharomyces cerevisiae YJM1573' save_ save__ma_target_ref_db_details.seq_db_align_begin _item_description.description ; Beginning index in the chemical sequence from the reference database. ; _item.name '_ma_target_ref_db_details.seq_db_align_begin' _item.category_id ma_target_ref_db_details _item.mandatory_code no _item_type.code code loop_ _item_examples.case '1' '2' save_ save__ma_target_ref_db_details.seq_db_align_end _item_description.description ; Ending index in the chemical sequence from the reference database. ; _item.name '_ma_target_ref_db_details.seq_db_align_end' _item.category_id ma_target_ref_db_details _item.mandatory_code no _item_type.code code loop_ _item_examples.case '105' '245' save_ save__ma_target_ref_db_details.seq_db_isoform _item_description.description ; Database code assigned by the reference database for a sequence isoform. An isoform sequence is an alternative protein sequence that can be generated from the same gene by a single or by a combination of biological events such as: alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting. ; _item.name '_ma_target_ref_db_details.seq_db_isoform' _item.category_id ma_target_ref_db_details _item.mandatory_code no _item_type.code code loop_ _item_examples.case 'P29994-6' save_ save__ma_target_ref_db_details.target_entity_id _item_description.description ; An identifier for the target entity. ; _item.name '_ma_target_ref_db_details.target_entity_id' _item.category_id ma_target_ref_db_details _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ma_target_ref_db_details.target_entity_id' _item_linked.parent_name '_ma_target_entity.entity_id' save_ save__ma_target_ref_db_details.gene_name _item_description.description ; Name of the gene corresponding to the target entity. ; _item.name '_ma_target_ref_db_details.gene_name' _item.category_id ma_target_ref_db_details _item.mandatory_code no _item_aliases.alias_name '_af_target_ref_db_details.gene' _item_aliases.dictionary 'mmcif_ma.dic' _item_aliases.version 1.3.3 _item_type.code code _item_examples.case 'bach1b' save_ save__ma_target_ref_db_details.seq_db_sequence_checksum _item_description.description ; Checksum (CRC64) for the sequence in the reference sequence database. ; _item.name '_ma_target_ref_db_details.seq_db_sequence_checksum' _item.category_id ma_target_ref_db_details _item.mandatory_code no _item_type.code code _item_examples.case 'EAB5441A9AF8E49E' save_ save__ma_target_ref_db_details.seq_db_sequence_version_date _item_description.description ; The version date of the sequence in the reference sequence database. ; _item.name '_ma_target_ref_db_details.seq_db_sequence_version_date' _item.category_id ma_target_ref_db_details _item.mandatory_code no _item_type.code yyyy-mm-dd _item_examples.case 2014-07-09 save_ ## TO BE REMOVED AT A LATER DATE ## ################################### save_af_target_ref_db_details _category.description ; Data items in the AF_TARGET_REF_DB_DETAILS category record details about the reference databases for the target sequences. This is due to be superceded by the _ma_target_ref_db_details category. ; _category.id af_target_ref_db_details _category.mandatory_code no _category_key.name '_af_target_ref_db_details.seq_db_sequence_checksum' _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id af_target_ref_db_details save_ save__af_target_ref_db_details.gene _item_description.description ; Name of the gene corresponding to the target entity. ; _item.name '_af_target_ref_db_details.gene' _item.category_id af_target_ref_db_details _item.mandatory_code no _item_type.code code _item_examples.case 'bach1b' save_ save__af_target_ref_db_details.seq_db_sequence_checksum _item_description.description ; Checksum (CRC64) for the sequence in the reference sequence database. ; _item.name '_af_target_ref_db_details.seq_db_sequence_checksum' _item.category_id af_target_ref_db_details _item.mandatory_code yes _item_type.code code _item_examples.case 'EAB5441A9AF8E49E' save_ save__af_target_ref_db_details.seq_db_sequence_version_date _item_description.description ; The version date of the sequence in the reference sequence database. ; _item.name '_af_target_ref_db_details.seq_db_sequence_version_date' _item.category_id af_target_ref_db_details _item.mandatory_code no _item_type.code yyyy-mm-dd _item_examples.case 2014-07-09 save_ ################################### ############# ## MA_DATA ## ############# save_ma_data _category.description ; Data items in the MA_DATA category capture the different kinds of data used in the modeling. These can be multiple sequence alignments, spatial restraints, template structures etc. ; _category.id ma_data _category.mandatory_code yes loop_ _category_key.name '_ma_data.id' loop_ _category_group.id 'inclusive_group' 'ma_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _ma_data.content_type "model coordinates" _ma_data.content_type_other_details ;DISCLAIMERS ALPHAFOLD DATA, COPYRIGHT (2021) DEEPMIND TECHNOLOGIES LIMITED. THE INFORMATION PROVIDED IS THEORETICAL MODELLING ONLY AND CAUTION SHOULD BE EXERCISED IN ITS USE. IT IS PROVIDED "AS-IS" WITHOUT ANY WARRANTY OF ANY KIND, WHETHER EXPRESSED OR IMPLIED. NO WARRANTY IS GIVEN THAT USE OF THE INFORMATION SHALL NOT INFRINGE THE RIGHTS OF ANY THIRD PARTY. THE INFORMATION IS NOT INTENDED TO BE A SUBSTITUTE FOR PROFESSIONAL MEDICAL ADVICE, DIAGNOSIS, OR TREATMENT, AND DOES NOT CONSTITUTE MEDICAL OR OTHER PROFESSIONAL ADVICE. IT IS AVAILABLE FOR ACADEMIC AND COMMERCIAL PURPOSES, UNDER CC-BY 4.0 LICENCE. ; _ma_data.id 1 _ma_data.name Model ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ma_data save_ save__ma_data.content_type _item_description.description ; The type of data held in the dataset. ; _item.name '_ma_data.content_type' _item.category_id ma_data _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value 'coevolution MSA' 'model coordinates' 'other' 'polymeric template library' 'spatial restraints' 'target' 'target-template alignment' 'template structure' save_ save__ma_data.content_type_other_details _item_description.description ; Details for other content types. ; _item.name '_ma_data.content_type_other_details' _item.category_id ma_data _item.mandatory_code no _item_type.code text save_ save__ma_data.id _item_description.description ; A unique identifier for the data. ; _item.name '_ma_data.id' _item.category_id ma_data _item.mandatory_code yes _item_type.code int save_ save__ma_data.name _item_description.description ; An author-given name for the content held in the dataset. ; _item.name '_ma_data.name' _item.category_id ma_data _item.mandatory_code yes _item_type.code line loop_ _item_examples.case 'Coevolution Data' 'Model' 'NMR NOE Distances' 'Target Template Alignment' save_ ################### ## MA_MODEL_LIST ## ################### save_ma_model_list _category.description ; Data items in the MA_MODEL_LIST category record the details of the models being deposited. ; _category.id ma_model_list _category.mandatory_code no loop_ _category_key.name '_ma_model_list.ordinal_id' loop_ _category_group.id 'inclusive_group' 'ma_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _ma_model_list.data_id 1 _ma_model_list.model_group_id 1 _ma_model_list.model_group_name "AlphaFold model" _ma_model_list.model_id 1 _ma_model_list.model_name "Top ranked model" _ma_model_list.model_type "Ab initio model" _ma_model_list.ordinal_id 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ma_model_list save_ save__ma_model_list.data_id _item_description.description ; The data_id identifier. This data item is a pointer to _ma_data.id in the MA_DATA category. ; _item.name '_ma_model_list.data_id' _item.category_id ma_model_list _item.mandatory_code yes _item_type.code int _item_linked.child_name '_ma_model_list.data_id' _item_linked.parent_name '_ma_data.id' save_ save__ma_model_list.model_group_id _item_description.description ; An identifier to group structural models into collections or sets. A cluster of models and its representative can either be grouped together or can be separate groups in the ma_model_list table. The choice between the two options should be decided based on how the modeling was carried out and how the representative was chosen. If the representative is a member of the ensemble (i.e., best scoring model), then it is recommended that the representative and the ensemble belong to the same model group. If the representative is calculated from the ensemble (i.e., centroid), then it is recommended that the representative be separated into a different group. If the models do not need to be grouped into collections, then the _ma_model_list.model_group_id is the same as _ma_model_list.model_id. ; _item.name '_ma_model_list.model_group_id' _item.category_id ma_model_list _item.mandatory_code no _item_type.code int save_ save__ma_model_list.model_group_name _item_description.description ; A decsriptive name for the model group. ; _item.name '_ma_model_list.model_group_name' _item.category_id ma_model_list _item.mandatory_code no _item_type.code line loop_ _item_examples.case 'AlphaFold model' 'cluster1' 'cluster2' save_ save__ma_model_list.model_id _item_description.description ; A unique identifier for the structural model being deposited. ; _item.name '_ma_model_list.model_id' _item.category_id ma_model_list _item.mandatory_code yes _item_type.code int _item_linked.parent_name '_ma_model_list.model_id' _item_linked.child_name '_atom_site.pdbx_PDB_model_num' save_ save__ma_model_list.model_name _item_description.description ; A decsriptive name for the model. ; _item.name '_ma_model_list.model_name' _item.category_id ma_model_list _item.mandatory_code no _item_type.code line loop_ _item_examples.case '2nd best scoring model' 'Best scoring model' 'Cluster center' 'Top ranked model' save_ save__ma_model_list.model_type _item_description.description ; The type of model. ; _item.name '_ma_model_list.model_type' _item.category_id ma_model_list _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail 'Ab initio model' 'Ab initio or template-free models' 'Homology model' 'Homology or comparative model based on existing templates' 'Other' 'Other computational models' save_ save__ma_model_list.ordinal_id _item_description.description ; A unique identifier for the model / model group combination. ; _item.name '_ma_model_list.ordinal_id' _item.category_id ma_model_list _item.mandatory_code yes _item_type.code int save_ ################## ## MA_QA_METRIC ## ################## save_ma_qa_metric _category.description ; Data items in the MA_QA_METRIC category record the details of the metrics use to assess model quality. ; _category.id ma_qa_metric _category.mandatory_code no loop_ _category_key.name '_ma_qa_metric.id' loop_ _category_group.id 'inclusive_group' 'ma_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; loop_ _ma_qa_metric.id _ma_qa_metric.mode _ma_qa_metric.name _ma_qa_metric.software_group_id _ma_qa_metric.type 1 global pLDDT 1 other 2 local pLDDT 1 other ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ma_qa_metric save_ save__ma_qa_metric.id _item_description.description ; An identifier for the QA metric. ; _item.name '_ma_qa_metric.id' _item.category_id ma_qa_metric _item.mandatory_code yes _item_type.code int save_ save__ma_qa_metric.mode _item_description.description ; The mode of calculation of the QA metric. ; _item.name '_ma_qa_metric.mode' _item.category_id ma_qa_metric _item.mandatory_code yes _item_type.code code loop_ _item_enumeration.value _item_enumeration.detail 'local' 'QA metric is calculated per-residue' 'global' 'QA metric is calculated per-model' 'local-pairwise' 'QA metric is calculated per-residue-pair' save_ save__ma_qa_metric.name _item_description.description ; Name of the QA metric. ; _item.name '_ma_qa_metric.name' _item.category_id ma_qa_metric _item.mandatory_code yes _item_type.code line save_ save__ma_qa_metric.software_group_id _item_description.description ; Identifier to the set of software used to calculate the QA metric. This data item is a pointer to the _ma_software_group.group_id in the MA_SOFTWARE_GROUP category. ; _item.name '_ma_qa_metric.software_group_id' _item.category_id ma_qa_metric _item.mandatory_code no _item_type.code int _item_linked.child_name '_ma_qa_metric.software_group_id' _item_linked.parent_name '_ma_software_group.group_id' save_ save__ma_qa_metric.type _item_description.description ; The type of QA metric. ; _item.name '_ma_qa_metric.type' _item.category_id ma_qa_metric _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail 'contact probability' 'the contact probability of a pairwise interaction' 'distance' 'the lower the distance, the better the quality' 'energy' 'the lower the energy, the better the quality' 'normalized score' 'normalized score ranging from 0 to 1' 'other' 'other type of QA metric' 'PAE' 'predicted aligned error' 'pLDDT' 'per-residue confidence score based on the Local Distance Difference Test' 'zscore' 'number of standard deviations from optimal/best' save_ ######################### ## MA_QA_METRIC_GLOBAL ## ######################### save_ma_qa_metric_global _category.description ; Data items in the MA_QA_METRIC_GLOBAL category captures the details of the global QA metrics, calculated at the model-level. ; _category.id ma_qa_metric_global _category.mandatory_code no loop_ _category_key.name '_ma_qa_metric_global.ordinal_id' loop_ _category_group.id 'inclusive_group' 'ma_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _ma_qa_metric_global.metric_id 1 _ma_qa_metric_global.metric_value 82.24 _ma_qa_metric_global.model_id 1 _ma_qa_metric_global.ordinal_id 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ma_qa_metric_global save_ save__ma_qa_metric_global.metric_id _item_description.description ; The identifier for the QA metric. This data item is a pointer to _ma_qa_metric.id in the MA_QA_METRIC category. ; _item.name '_ma_qa_metric_global.metric_id' _item.category_id ma_qa_metric_global _item.mandatory_code yes _item_type.code int _item_linked.child_name '_ma_qa_metric_global.metric_id' _item_linked.parent_name '_ma_qa_metric.id' save_ save__ma_qa_metric_global.metric_value _item_description.description ; The value of the global QA metric. ; _item.name '_ma_qa_metric_global.metric_value' _item.category_id ma_qa_metric_global _item.mandatory_code yes _item_type.code float save_ save__ma_qa_metric_global.model_id _item_description.description ; The identifier for the structural model, for which global QA metric is provided. This data item is a pointer to _ma_model_list.model_id in the MA_MODEL_LIST category. ; _item.name '_ma_qa_metric_global.model_id' _item.category_id ma_qa_metric_global _item.mandatory_code yes _item_type.code int _item_linked.child_name '_ma_qa_metric_global.model_id' _item_linked.parent_name '_ma_model_list.model_id' save_ save__ma_qa_metric_global.ordinal_id _item_description.description ; A unique identifier for the category. ; _item.name '_ma_qa_metric_global.ordinal_id' _item.category_id ma_qa_metric_global _item.mandatory_code yes _item_type.code int save_ ######################## ## MA_QA_METRIC_LOCAL ## ######################## save_ma_qa_metric_local _category.description ; Data items in the MA_QA_METRIC_LOCAL category captures the details of the local QA metrics, calculated at the residue-level. ; _category.id ma_qa_metric_local _category.mandatory_code no loop_ _category_key.name '_ma_qa_metric_local.label_asym_id' '_ma_qa_metric_local.label_comp_id' '_ma_qa_metric_local.label_seq_id' loop_ _category_group.id 'inclusive_group' 'ma_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; loop_ _ma_qa_metric_local.label_asym_id _ma_qa_metric_local.label_comp_id _ma_qa_metric_local.label_seq_id _ma_qa_metric_local.metric_id _ma_qa_metric_local.metric_value _ma_qa_metric_local.model_id _ma_qa_metric_local.ordinal_id A MET 1 2 63.75 1 1 A ALA 2 2 66.38 1 1 A GLY 3 2 65.17 1 1 A GLU 4 2 65.58 1 1 A LEU 5 2 67.12 1 1 A VAL 6 2 68.35 1 1 A SER 7 2 67.54 1 1 # - - - - data truncated for brevity - - - - ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ma_qa_metric_local save_ save__ma_qa_metric_local.label_asym_id _item_description.description ; The identifier for the asym id of the residue in the structural model, for which local QA metric is provided. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category. ; _item.name '_ma_qa_metric_local.label_asym_id' _item.category_id ma_qa_metric_local _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ma_qa_metric_local.label_asym_id' _item_linked.parent_name '_atom_site.label_asym_id' save_ save__ma_qa_metric_local.label_comp_id _item_description.description ; The component identifier for the residue in the structural model, for which local QA metric is provided. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category. ; _item.name '_ma_qa_metric_local.label_comp_id' _item.category_id ma_qa_metric_local _item.mandatory_code yes _item_type.code ucode _item_linked.child_name '_ma_qa_metric_local.label_comp_id' _item_linked.parent_name '_atom_site.label_comp_id' save_ save__ma_qa_metric_local.label_seq_id _item_description.description ; The identifier for the sequence index of the residue in the structural model, for which local QA metric is provided. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category. ; _item.name '_ma_qa_metric_local.label_seq_id' _item.category_id ma_qa_metric_local _item.mandatory_code yes _item_type.code int _item_linked.child_name '_ma_qa_metric_local.label_seq_id' _item_linked.parent_name '_atom_site.label_seq_id' save_ save__ma_qa_metric_local.metric_id _item_description.description ; The identifier for the QA metric. This data item is a pointer to _ma_qa_metric.id in the MA_QA_METRIC category. ; _item.name '_ma_qa_metric_local.metric_id' _item.category_id ma_qa_metric_local _item.mandatory_code yes _item_type.code int _item_linked.child_name '_ma_qa_metric_local.metric_id' _item_linked.parent_name '_ma_qa_metric.id' save_ save__ma_qa_metric_local.metric_value _item_description.description ; The value of the local QA metric. ; _item.name '_ma_qa_metric_local.metric_value' _item.category_id ma_qa_metric_local _item.mandatory_code yes _item_type.code float save_ save__ma_qa_metric_local.model_id _item_description.description ; The identifier for the structural model, for which local QA metric is provided. This data item is a pointer to _ma_model_list.model_id in the MA_MODEL_LIST category. ; _item.name '_ma_qa_metric_local.model_id' _item.category_id ma_qa_metric_local _item.mandatory_code yes _item_type.code int _item_linked.child_name '_ma_qa_metric_local.model_id' _item_linked.parent_name '_ma_model_list.model_id' save_ save__ma_qa_metric_local.ordinal_id _item_description.description ; A unique identifier for the category. ; _item.name '_ma_qa_metric_local.ordinal_id' _item.category_id ma_qa_metric_local _item.mandatory_code yes _item_type.code int save_ ####################### ## MA_SOFTWARE_GROUP ## ####################### save_ma_software_group _category.description ; Data items in the MA_SOFTWARE_GROUP category describes the collection of software into groups so that they can be used efficiently in the MA_PROTOCOL_STEP category. ; _category.id ma_software_group _category.mandatory_code yes loop_ _category_key.name '_ma_software_group.ordinal_id' loop_ _category_group.id 'inclusive_group' 'ma_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _ma_software_group.group_id 1 _ma_software_group.ordinal_id 1 _ma_software_group.software_id 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ma_software_group save_ save__ma_software_group.group_id _item_description.description ; An identifier for the group entry. If data does not need to be grouped, then _ma_software_group.group_id is the same as _ma_software_group.software_id. ; _item.name '_ma_software_group.group_id' _item.category_id ma_software_group _item.mandatory_code yes _item_type.code int save_ save__ma_software_group.ordinal_id _item_description.description ; A unique identifier for the category. ; _item.name '_ma_software_group.ordinal_id' _item.category_id ma_software_group _item.mandatory_code yes _item_type.code int save_ save__ma_software_group.software_id _item_description.description ; The identifier for the software. This data item is a pointer to _software.pdbx_ordinal in the SOFTWARE category. ; _item.name '_ma_software_group.software_id' _item.category_id ma_software_group _item.mandatory_code yes _item_type.code int _item_linked.child_name '_ma_software_group.software_id' _item_linked.parent_name '_software.pdbx_ordinal' save_ ###################### ## MA_TARGET_ENTITY ## ###################### save_ma_target_entity _category.description ; Data items in the MA_TARGET_ENTITY category record details about the target entities. The details are provided for each entity being modeled. ; _category.id ma_target_entity _category.mandatory_code no _category_key.name '_ma_target_entity.entity_id' loop_ _category_group.id 'inclusive_group' 'ma_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _ma_target_entity.data_id 1 _ma_target_entity.entity_id 1 _ma_target_entity.origin "reference database" ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ma_target_entity save_ save__ma_target_entity.data_id _item_description.description ; The data_id identifier. This data item is a pointer to _ma_data.id in the MA_DATA category. ; _item.name '_ma_target_entity.data_id' _item.category_id ma_target_entity _item.mandatory_code yes _item_type.code int _item_linked.child_name '_ma_target_entity.data_id' _item_linked.parent_name '_ma_data.id' save_ save__ma_target_entity.entity_id _item_description.description ; A unique identifier for the distinct molecular entity of the target. This data item is a pointer to _entity.id in the ENTITY category. ; _item.name '_ma_target_entity.entity_id' _item.category_id ma_target_entity _item.mandatory_code yes _item_type.code code _item_linked.child_name '_ma_target_entity.entity_id' _item_linked.parent_name '_entity.id' save_ save__ma_target_entity.origin _item_description.description ; The origin of the target entity. ; _item.name '_ma_target_entity.origin' _item.category_id ma_target_entity _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail 'reference database' 'target is obtained from an exisiting reference database' 'designed' 'target is designed by the user' save_ ############################### ## MA_TARGET_ENTITY_INSTANCE ## ############################### save_ma_target_entity_instance _category.description ; Data items in the MA_TARGET_ENTITY_INSTANCE category record details about the instances of target entities modeled. ; _category.id ma_target_entity_instance _category.mandatory_code no _category_key.name '_ma_target_entity_instance.asym_id' loop_ _category_group.id 'inclusive_group' 'ma_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on AFDB entry AF-Q8W3K0-F1. ; ; _ma_target_entity_instance.asym_id A _ma_target_entity_instance.details . _ma_target_entity_instance.entity_id 1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _pdbx_category_context.type CONTRIBUTED _pdbx_category_context.category_id ma_target_entity_instance save_ save__ma_target_entity_instance.asym_id _item_description.description ; A unique identifier for the instance of the entity. ; _item.name '_ma_target_entity_instance.asym_id' _item.category_id ma_target_entity_instance _item.mandatory_code yes _item_type.code code _item_linked.child_name '_struct_asym.id' _item_linked.parent_name '_ma_target_entity_instance.asym_id' save_ save__ma_target_entity_instance.details _item_description.description ; Additional details about the entity instance. ; _item.name '_ma_target_entity_instance.details' _item.category_id ma_target_entity_instance _item.mandatory_code no _item_type.code text save_ save__ma_target_entity_instance.entity_id _item_description.description ; A unique identifier for the distinct molecular entity of the target. This data item is a pointer to _ma_target_entity.entity_id in the MA_TARGET_ENTITY category. ; _item.name '_ma_target_entity_instance.entity_id' _item.category_id ma_target_entity_instance _item.mandatory_code yes _item_type.code code loop_ _item_linked.child_name _item_linked.parent_name '_ma_target_entity_instance.entity_id' '_ma_target_entity.entity_id' '_struct_asym.entity_id' '_ma_target_entity_instance.entity_id' save_