An example of an entity description:
loop_
_entity.id
_entity.type
_entity.formula_weight
_entity.details
1 polymer 10916
; The enzymatically competent form of HIV protease is a
dimer. This entity corresponds to one monomer of an
active dimer.
;
2 non-polymer 'need number here' '.'
3 water 18 '.'
#
loop_
_entity_name_com.entity_id
_entity_name_com.name
1 'HIV-1 protease monomer'
1 'HIV-1 PR monomer'
2 'acetyl-pepstatin'
2 'acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine'
3 'water'
#
loop_
_entity_src_gen.entity_id
_entity_src_gen.gene_src_common_name
_entity_src_gen.gene_src_strain
_entity_src_gen.host_org_common_name
_entity_src_gen.host_org_genus
_entity_src_gen.host_org_species
_entity_src_gen.plasmid_name
1 'HIV-1' 'NY-5' 'bacteria' 'Escherichia' 'coli' 'pB322'
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.
An abbreviated example of the description of a polymeric entity for a simple protein.
loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_chirality _entity_poly.nstd_linkage _entity_poly.nstd_monomer 1 polypeptide(L) no no no loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id 1 1 PRO 1 2 GLN 1 3 ILE 1 4 THR 1 5 LEU 1 6 TRP 1 7 GLN 1 8 ARG 1 9 PRO 1 10 LEU 1 11 VAL 1 12 THR 1 13 ILE 1 14 LYS 1 15 ILE 1 16 GLY 1 17 GLY 1 18 GLN 1 19 LEU 1 20 LYS 1 21 GLU 1 22 ALA 1 23 LEU 1 24 LEU 1 25 ASP # # ---- abbreviated -----
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).
An abbreviated example for a drug-DNA complex illustrating both polymer and non-polymer entity descriptions:
loop_
_entity.id
_entity.type
_entity.src_method
1 polymer 'man'
2 non-polymer 'man'
3 water .
loop_
_entity_keywords.entity_id
_entity_keywords.text
1 'NUCLEIC ACID'
2 'DRUG'
loop_
_entity_name_com.entity_id
_entity_name_com.name
2 ADRIAMYCIN
3 WATER
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.mon_id
_entity_poly_seq.num
1 T 1
1 G 2
1 G 3
1 C 4
1 C 5
1 A 6
# ... Abbreviated ...
loop_
_entity_poly.entity_id
_entity_poly.number_of_monomers
_entity_poly.type
1 8 'polydeoxyribonucleotide'
loop_
_chem_comp.id
_chem_comp.name
A ADENINE
T THYMINE
C CYTOSINE
G GUANINE
DM2 ADRIAMYCIN
HOH WATER
loop_
_atom_site.id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_seq_id
_atom_site.label_entity_id
_atom_site.cartn_x
_atom_site.cartn_y
_atom_site.cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
1 O5* T A 1 1 -18.744 20.195 22.722 1.00 36.68
2 C5* T A 1 1 -18.262 20.915 23.867 1.00 4.63
# .... Abbreviated ....