Entry composition & details
| PDBx/mmCIF category | Legacy PDB format records | Description |
|---|---|---|
| _entity | COMPOUND | Details about each unique molecular entity (protein, nucleic acid, carbohydrate, small molecule) present in the structure. |
Example:
| loop_ | |||||||||
| _entity.id | |||||||||
| _entity.type | |||||||||
| _entity.src_method | |||||||||
| _entity.pdbx_description | |||||||||
| _entity.formula_weight | |||||||||
| _entity.pdbx_number_of_molecules | |||||||||
| _entity.pdbx_ec | |||||||||
| _entity.pdbx_mutation | |||||||||
| _entity.pdbx_fragment | |||||||||
| _entity.details | |||||||||
| 1 | polymer | man | '3C-like proteinase' | 33825.547 | 1 | 3.4.22.69 | ? | ? | ? |
| 2 | non-polymer | syn | |||||||
| ;(1R,2S,5S)-N-{(1E,2S)-1-imino-3[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl- | |||||||||
| 3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide | |||||||||
| ; | |||||||||
| 501.542 | 1 | ? | ? | ? | ? | ||||
| 3 | water | nat | water | 18.015 | 83 | ? | ? | ? | ? |
| PDBx/mmCIF category | Legacy PDB format records | Description |
|---|---|---|
| _pdbx_entity_nonpoly | N/A | Provides mapping between entity and the non polymer component. |
Example:
| loop_ | ||
| _pdbx_entity_nonpoly.entity_id | ||
| _pdbx_entity_nonpoly.name | ||
| _pdbx_entity_nonpoly.comp_id | ||
| 2 | ||
| ;(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl}-6,6-dimethyl- | ||
| 3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide | ||
| ; | ||
| 4WI | ||
| 3 | water | HOH |
| PDBx/mmCIF category | Legacy PDB format records | Description |
|---|---|---|
| _chem_comp |
|
Details about each of the chemical components from which the relevant chemical structures can be constructed, such as name, synonym, mass, or formula. |
Example:
| 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 | ||||||
| 4WI | non-polymer | . | ||||
| ;(1R,2S,5S)-N{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl- | ||||||
| 3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide | ||||||
| ; | ||||||
| 'PF-07321332, bound form; nirmatrelvir, bound form; Paxlovid, bound form' 'C23 H34 F3 | ||||||
| N5 O4' 501.542 | ||||||
| ALA | 'L-peptide linking' | y | ALANINE | ? | 'C3 H7 N O2' | 89.093 |
| ARG | 'L-peptide linking' | y | ARGININE | ? | 'C6 H15 N4 O2 1' | 175.209 |
| ASN | 'L-peptide linking' | y | ASPARAGINE | ? | 'C4 H8 N2 O3' | 132.118 |
| ASP | 'L-peptide linking' | y | 'ASPARTIC ACID' | ? | 'C4 H7 N O4' | 133.103 |
| ... (truncated for brevity) | ||||||
| PDBx/mmCIF category | Legacy PDB format records | Description |
|---|---|---|
| _pdbx_nonpoly_scheme | N/A | Residue level nomenclature mapping for non-polymer entities. |
Example:
| loop_ | |||||||||
| _pdbx_nonpoly_scheme.asym_id | |||||||||
| _pdbx_nonpoly_scheme.entity_id | |||||||||
| _pdbx_nonpoly_scheme.mon_id | |||||||||
| _pdbx_nonpoly_scheme.ndb_seq_num | |||||||||
| _pdbx_nonpoly_scheme.pdb_seq_num | |||||||||
| _pdbx_nonpoly_scheme.auth_seq_num | |||||||||
| _pdbx_nonpoly_scheme.pdb_mon_id | |||||||||
| _pdbx_nonpoly_scheme.auth_mon_id | |||||||||
| _pdbx_nonpoly_scheme.pdb_strand_id | |||||||||
| _pdbx_nonpoly_scheme.pdb_ins_code | |||||||||
| B | 2 | 4WI | 1 | 401 | 1 | 4WI | UNL | A | . |
| C | 3 | HOH | 1 | 501 | 12 | HOH | HOH | A | . |
| C | 3 | HOH | 2 | 502 | 85 | HOH | HOH | A | . |
| C | 3 | HOH | 3 | 503 | 52 | HOH | HOH | A | . |
| C | 3 | HOH | 4 | 504 | 27 | HOH | HOH | A | . |
| C | 3 | HOH | 5 | 505 | 29 | HOH | HOH | A | . |
| C | 3 | HOH | 6 | 506 | 3 | HOH | HOH | A | . |
| C | 3 | HOH | 7 | 507 | 23 | HOH | HOH | A | . |
| C | 3 | HOH | 8 | 508 | 55 | HOH | HOH | A | . |
| C | 3 | HOH | 9 | 509 | 42 | HOH | HOH | A | . |
| C | 3 | HOH | 10 | 510 | 53 | HOH | HOH | A | . |
| ... (truncated for brevity) | |||||||||
Connectivity
| PDBx/mmCIF category | Legacy PDB format records | Description |
|---|---|---|
| _struct_conn | LINK | Details about the connections between portions of the structure. These can be covalent bonds, disulfide bridges, hydrogen bonds, and so on. |
Example:
| _struct_conn.id | covale1 |
| _struct_conn.conn_type_id | covale |
| _struct_conn.pdbx_leaving_atom_flag | none |
| _struct_conn.pdbx_PDB_id | ? |
| _struct_conn.ptnr1_label_asym_id | A |
| _struct_conn.ptnr1_label_comp_id | CYS |
| _struct_conn.ptnr1_label_seq_id | 145 |
| _struct_conn.ptnr1_label_atom_id | SG |
| _struct_conn.pdbx_ptnr1_label_alt_id | ? |
| _struct_conn.pdbx_ptnr1_PDB_ins_code | ? |
| _struct_conn.pdbx_ptnr1_standard_comp_id | ? |
| _struct_conn.ptnr1_symmetry | 1_555 |
| _struct_conn.ptnr2_label_asym_id | B |
| _struct_conn.ptnr2_label_comp_id | 4WI |
| _struct_conn.ptnr2_label_seq_id | . |
| _struct_conn.ptnr2_label_atom_id | C3 |
| _struct_conn.pdbx_ptnr2_label_alt_id | ? |
| _struct_conn.pdbx_ptnr2_PDB_ins_code | ? |
| _struct_conn.ptnr1_auth_asym_id | A |
| _struct_conn.ptnr1_auth_comp_id | CYS |
| _struct_conn.ptnr1_auth_seq_id | 145 |
| _struct_conn.ptnr2_auth_asym_id | A |
| _struct_conn.ptnr2_auth_comp_id | 4WI |
| _struct_conn.ptnr2_auth_seq_id | 401 |
| _struct_conn.ptnr2_symmetry | 1_555 |
| _struct_conn.pdbx_ptnr3_label_atom_id | ? |
| _struct_conn.pdbx_ptnr3_label_seq_id | ? |
| _struct_conn.pdbx_ptnr3_label_comp_id | ? |
| _struct_conn.pdbx_ptnr3_label_asym_id | ? |
| _struct_conn.pdbx_ptnr3_label_alt_id | ? |
| _struct_conn.pdbx_ptnr3_PDB_ins_code | ? |
| _struct_conn.details | ? |
| _struct_conn.pdbx_dist_value | 1.804 |
| _struct_conn.pdbx_value_order | ? |
| _struct_conn.pdbx_role | ? |
| PDBx/mmCIF category | Legacy PDB format records | Description |
|---|---|---|
| _chem_comp_bond | N/A | Details about the bonds and bond orders between atoms in a chemical component. |
Example:
| loop_ | ||||||
| _chem_comp_bond.comp_id | ||||||
| _chem_comp_bond.atom_id_1 | ||||||
| _chem_comp_bond.atom_id_2 | ||||||
| _chem_comp_bond.value_order | ||||||
| _chem_comp_bond.pdbx_aromatic_flag | ||||||
| _chem_comp_bond.pdbx_stereo_config | ||||||
| _chem_comp_bond.pdbx_ordinal | ||||||
| 4WI | O1 | C8 | doub | N | N | 1 |
| 4WI | C8 | N2 | sing | N | N | 2 |
| 4WI | C8 | C5 | sing | N | N | 3 |
| 4WI | N2 | C7 | sing | N | N | 4 |
| 4WI | C4 | C5 | sing | N | N | 5 |
| 4WI | C4 | C2 | sing | N | N | 6 |
| 4WI | C5 | C6 | sing | N | N | 7 |
| 4WI | N5 | C3 | doub | N | N | 8 |
| 4WI | C3 | C2 | sing | N | N | 9 |
| 4WI | C7 | C6 | sing | N | N | 10 |
| 4WI | C2 | N1 | sing | N | N | 11 |
| 4WI | N2 | H9 | sing | N | N | 69 |
| ... (truncated for brevity) | ||||||
| PDBx/mmCIF category | Legacy PDB format records | Description |
|---|---|---|
| _chem_comp_atom | N/A | Details about the atoms in a chemical component. |
Example:
| loop_ | |||||
| _chem_comp_atom.comp_id | |||||
| _chem_comp_atom.atom_id | |||||
| _chem_comp_atom.type_symbol | |||||
| _chem_comp_atom.pdbx_aromatic_flag | |||||
| _chem_comp_atom.pdbx_stereo_config | |||||
| _chem_comp_atom.pdbx_ordinal | |||||
| 4WI | C8 | C | N | N | 1 |
| 4WI | C3 | C | N | N | 2 |
| 4WI | C1 | C | N | N | 3 |
| 4WI | C13 | C | N | N | 4 |
| 4WI | C21 | C | N | N | 5 |
| 4WI | C6 | C | N | N | 6 |
| 4WI | C7 | C | N | N | 7 |
| 4WI | C10 | C | N | N | 8 |
| 4WI | C5 | C | N | S | 9 |
| 4WI | C9 | C | N | S | 10 |
| 4WI | C11 | C | N | S | 11 |
| ... (truncated for brevity) | |||||