Data Items Describing Molecular Entities
A molecular entity is a chemically distinct part of an mmCIF entry. There are three types of entities: polymer, non-polymer, and water. A common name, systematic name, source and taxonomy information, expression details, and keyword description can be assigned to each mmCIF entity. The categories that describe these entity features are shown schematically in the following diagram.
Data Category Relationships for the ENTITY Category
Click-on data items in the figure to navigate to more details about the item.
ENTITY Example
The following is a typical example of the ENTITY and related categories found in a recent PDB entry, 4N03.
loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.details 1 polymer man 'ABC-type branched-chain amino acid transport systems periplasmic component-like protein' 43344.293 1 ? 2 non-polymer syn 'PALMITIC ACID' 256.428 1 ? 3 non-polymer syn 1,2-ETHANEDIOL 62.068 1 ? 4 water nat water 18.015 467 ? # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_gene_src_gene 'NC_013510.1:3663026..3664297, Tcur_3166' _entity_src_gen.gene_src_strain 'DSM 43183' _entity_src_gen.pdbx_gene_src_scientific_name 'Thermomonospora curvata' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 471852 _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)' _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.plasmid_name pMCSG68
Polymer and Non-polymer Molecular Entities
Additional categories are provided to describe polymeric entities. Polymer type, one-letter code polymer sequences, sequence length, information about non-standard linkages and chirality may be specified. In the _entity_poly.pdbx_seq_one_letter_code sequence, modified residues are identified by their 3-letter codes within parentheses. In the _entity_poly.pdbx_seq_one_letter_code_can sequence, modified residues are identified by either the one-letter code of the parent residue or by one of the conventional one-letter code placeholders X or N as appropriate. The PDB chain identifiers corresponding to each polymer entity are provided as a comma-separated list in data item _entity_poly.pdbx_strand_id. The monomer sequence for each polymer entity is listed in category ENTITY_POLY_SEQ. This sequence information is directly linked to the sequence specified in the coordinate list. It is also linked to the full chemical description of each monomer or non-standard monomer in the CHEM_COMP category group. The mmCIF categories describing polymer entities are shown schematically in the following diagram.
Non-polymeric entities are treated as individual chemical components. These entities may be fully described in the CHEM_COMP group of categories in the same manner as monomers within a polymeric entity. Like polymeric entities, each non-polymeric entity carries both an entity identifier and a component identifier. These identifiers form part of the label used to identify each atom (_atom_site.label_entity_id and _atom_site.label_comp_id). For polymeric entities the the monomer identifier and the component identifier are the same; however, the atom label also includes an additional field for the sequence position (
_atom_site.label_seq_id).
Data Category Relationships for the ENTITY_POLY Category
Click-on data items in the figure to navigate to more details about the item.
ENTITY_POLY Example
An abbreviated example of the description of a polymeric entity from PDB entry 4N03.
# _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;SNAAGCSSDKATGGSEATGPDGVKQGPGVTDKTIKLGIATDLTGVYAPLGKSITQAQQLYYEEVNQRGGVCGRTIEAVVR DHGYDPQKAVSIYTELNNNVLAIPHFLGSP(MSE)VSAVKQRIESDK(MSE)FTIPSAWTTALLGSKYIQVTGTTYDVD (MSE)INGVQWL(MSE)DKKLIKKGDKLGHVYFEGDYGGSALRGTKYAAEQLGLEVFELPIKPTDRD(MSE)KSQVAALA KEKVDAILLSAGPQQAASLAGIARSQG(MSE)KQPILGSNSAYSPQLLATPAKPALVEGFFIATAGAP(MSE)SADLPAI KKLAEAYSKKYPKDPLDSGVVNGYGGASIVVSALEKACANKDLTREGLINAHRSEANADDGLGTP(MSE)NFTYFDKPAT RKTYIIKPDEKATGGAVIVEQAFESELAKNYQVPVGTF ; _entity_poly.pdbx_seq_one_letter_code_can ;SNAAGCSSDKATGGSEATGPDGVKQGPGVTDKTIKLGIATDLTGVYAPLGKSITQAQQLYYEEVNQRGGVCGRTIEAVVR DHGYDPQKAVSIYTELNNNVLAIPHFLGSPMVSAVKQRIESDKMFTIPSAWTTALLGSKYIQVTGTTYDVDMINGVQWLM DKKLIKKGDKLGHVYFEGDYGGSALRGTKYAAEQLGLEVFELPIKPTDRDMKSQVAALAKEKVDAILLSAGPQQAASLAG IARSQGMKQPILGSNSAYSPQLLATPAKPALVEGFFIATAGAPMSADLPAIKKLAEAYSKKYPKDPLDSGVVNGYGGASI VVSALEKACANKDLTREGLINAHRSEANADDGLGTPMNFTYFDKPATRKTYIIKPDEKATGGAVIVEQAFESELAKNYQV PVGTF ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier MCSG-APC111258 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 SER n 1 2 ASN n 1 3 ALA n 1 4 ALA n 1 5 GLY n 1 6 CYS n 1 7 SER n 1 8 SER n 1 9 ASP n 1 10 LYS n 1 11 ALA n 1 12 THR n 1 13 GLY n 1 14 GLY n 1 15 SER n 1 16 GLU n 1 17 ALA n 1 18 THR n 1 19 GLY n 1 20 PRO n 1 21 ASP n 1 22 GLY n 1 23 VAL n # ---- Abbreviated ---- loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.094 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.120 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.132 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.104 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.147 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.197 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.146 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.174 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.174 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.191 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.130 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.119 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.210 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.154 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.164 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.191 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 SE' 196.107 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.228 PLM NON-POLYMER . 'PALMITIC ACID' ? 'C16 H32 O2' 256.428 EDO NON-POLYMER . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 HOH NON-POLYMER . WATER ? 'H2 O' 18.015
Chimeric Polymer Molecular Entity Example
Fusion proteins and other chimeric polymeric molecular entities may be represented in a similar manner by
providing the mononer ranges applicable for each source organism assignment. In the following exammple for
PDB Entry 5HKJ, the segments of the fusion protein are described by the data items _entity_src_gen.pdbx_src_id,
_entity_src_gen.pdbx_beg_seq_num and _entity_src_gen.pdbx_end_seq_num.
In this example the corresponding reference sequence database accesion codes (e.g. UniProt P02745, P02747, P02746)
are also specified in the STRUCT_REF_SEQ data category.
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
1 polymer man 'C1q subunits A, C, and B' 45697.594 1
2 non-polymer man N-ACETYL-D-GLUCOSAMINE 221.208 1
3 non-polymer syn 'CALCIUM ION' 40.078 1
4 water nat water 18.015 231
#
_entity_poly.entity_id 1
_entity_poly.type 'polypeptide(L)'
_entity_poly.nstd_linkage no
_entity_poly.nstd_monomer no
_entity_poly.pdbx_seq_one_letter_code
;KDQPRPAFSAIRRNPPMGGNVVIFDTVITNQEEPYQNHSGRFVCTVPGYYYFTFQVLSQWEICLSIVSSSRGQVRRSLGF
CDTTNKGLFQVVSGGMVLQLQQGDQVWVEKDPKKGHIYQGSEADSVFSGFLIFPSAGSGKQKFQSVFTVTRQTHQPPAPN
SLIRFNAVLTNPQGDYDTSTGKFTCKVPGLYYFVYHASHTANLCVLLYRSGVKVVTFCGHTSKTNQVNSGGVLLRLQVGE
EVWLAVNDYYDMVGIQGSDSVFSGFLLFPDGSAKATQKIAFSATRTINVPLRRDQTIRFDHVITNMNNNYEPRSGKFTCK
VPGLYYFTYHASSRGNLCVNLMRGRERAQKVVTFCDYAYNTFQVTTGGMVLKLEQGENVFLQATDKNSLLGMEGANSIFS
GFLLFPDMEA
;
_entity_poly.pdbx_seq_one_letter_code_can
;KDQPRPAFSAIRRNPPMGGNVVIFDTVITNQEEPYQNHSGRFVCTVPGYYYFTFQVLSQWEICLSIVSSSRGQVRRSLGF
CDTTNKGLFQVVSGGMVLQLQQGDQVWVEKDPKKGHIYQGSEADSVFSGFLIFPSAGSGKQKFQSVFTVTRQTHQPPAPN
SLIRFNAVLTNPQGDYDTSTGKFTCKVPGLYYFVYHASHTANLCVLLYRSGVKVVTFCGHTSKTNQVNSGGVLLRLQVGE
EVWLAVNDYYDMVGIQGSDSVFSGFLLFPDGSAKATQKIAFSATRTINVPLRRDQTIRFDHVITNMNNNYEPRSGKFTCK
VPGLYYFTYHASSRGNLCVNLMRGRERAQKVVTFCDYAYNTFQVTTGGMVLKLEQGENVFLQATDKNSLLGMEGANSIFS
GFLLFPDMEA
;
_entity_poly.pdbx_strand_id A
_entity_poly.pdbx_target_identifier ?
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 LYS n
1 2 ASP n
1 3 GLN n
1 4 PRO n
1 5 ARG n
1 6 PRO n
1 7 ALA n
1 8 PHE n
1 9 SER n
1 10 ALA n
1 11 ILE n
1 12 ARG n
1 13 ARG n
1 14 ASN n
1 15 PRO n
1 16 PRO n
1 17 MET n
1 18 GLY n
1 19 GLY n
1 20 ASN n
# .... Abbreviated ....
loop_
_entity_src_gen.entity_id
_entity_src_gen.pdbx_src_id
_entity_src_gen.pdbx_alt_source_flag
_entity_src_gen.pdbx_seq_type
_entity_src_gen.pdbx_beg_seq_num
_entity_src_gen.pdbx_end_seq_num
_entity_src_gen.gene_src_common_name
_entity_src_gen.gene_src_genus
_entity_src_gen.pdbx_gene_src_gene
_entity_src_gen.pdbx_gene_src_scientific_name
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
_entity_src_gen.pdbx_host_org_scientific_name
_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
_entity_src_gen.pdbx_host_org_cell_line
_entity_src_gen.plasmid_name
1 1 sample 'Biological sequence' 1 136 Human ? C1QA 'Homo sapiens' 9606 'Homo sapiens' 9606 'HEK 293-F' pcDNA3.1
1 2 sample 'Biological sequence' 140 270 Human ? 'C1QC, C1QG' 'Homo sapiens' 9606 'Homo sapiens' 9606 'HEK 293-F' pcDNA3.1
1 3 sample 'Biological sequence' 271 410 Human ? C1QB 'Homo sapiens' 9606 'Homo sapiens' 9606 'HEK 293-F' pcDNA3.1
#
loop_
_struct_ref.id
_struct_ref.db_name
_struct_ref.db_code
_struct_ref.pdbx_db_accession
_struct_ref.pdbx_db_isoform
_struct_ref.entity_id
_struct_ref.pdbx_seq_one_letter_code
_struct_ref.pdbx_align_begin
1 UNP C1QA_HUMAN P02745 ? 1
;KDQPRPAFSAIRRNPPMGGNVVIFDTVITNQEEPYQNHSGRFVCTVPGYYYFTFQVLSQWEICLSIVSSSRGQVRRSLGF
CDTTNKGLFQVVSGGMVLQLQQGDQVWVEKDPKKGHIYQGSEADSVFSGFLIFPSA
;
110
2 UNP C1QC_HUMAN P02747 ? 1
;KQKFQSVFTVTRQTHQPPAPNSLIRFNAVLTNPQGDYDTSTGKFTCKVPGLYYFVYHASHTANLCVLLYRSGVKVVTFCG
HTSKTNQVNSGGVLLRLQVGEEVWLAVNDYYDMVGIQGSDSVFSGFLLFPD
;
115
3 UNP C1QB_HUMAN P02746 ? 1
;KATQKIAFSATRTINVPLRRDQTIRFDHVITNMNNNYEPRSGKFTCKVPGLYYFTYHASSRGNLCVNLMRGRERAQKVVT
FCDYAYNTFQVTTGGMVLKLEQGENVFLQATDKNSLLGMEGANSIFSGFLLFPDMEA
;
117
#