data_9AVQ # _model_server_result.job_id kOJQeIBI9Zis7WsyjgLzcA _model_server_result.datetime_utc '2024-11-14 16:48:44' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 9avq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 9AVQ # _exptl.entry_id 9AVQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 501.542 _entity.id 2 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description (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 _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 9AVQ _cell.length_a 45.74 _cell.length_b 64.52 _cell.length_c 105.19 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9AVQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 145 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 145 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C3 _struct_conn.ptnr2_label_comp_id 4WI _struct_conn.ptnr2_label_seq_id . _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_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.793 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C23 H34 F3 N5 O4' _chem_comp.formula_weight 501.542 _chem_comp.id 4WI _chem_comp.mon_nstd_flag . _chem_comp.name (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 _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'PF-07321332, bound form;nirmatrelvir, bound form;Paxlovid, bound form' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O1 C8 4WI doub 1 n n C8 N2 4WI sing 2 n n C8 C5 4WI sing 3 n n N2 C7 4WI sing 4 n n C4 C5 4WI sing 5 n n C4 C2 4WI sing 6 n n C5 C6 4WI sing 7 n n N5 C3 4WI doub 8 n n C3 C2 4WI sing 9 n n C7 C6 4WI sing 10 n n C2 N1 4WI sing 11 n n N1 C1 4WI sing 12 n n F1 C22 4WI sing 13 n n O3 C13 4WI doub 14 n n C1 C9 4WI sing 15 n n C1 O2 4WI doub 16 n n F3 C22 4WI sing 17 n n C23 C15 4WI sing 18 n n C22 F2 4WI sing 19 n n C22 C21 4WI sing 20 n n C9 N3 4WI sing 21 n n C9 C12 4WI sing 22 n n C13 N3 4WI sing 23 n n C13 C14 4WI sing 24 n n N4 C21 4WI sing 25 n n N4 C14 4WI sing 26 n n C19 C18 4WI sing 27 n n N3 C10 4WI sing 28 n n C21 O4 4WI doub 29 n n C12 C18 4WI sing 30 n n C12 C11 4WI sing 31 n n C14 C15 4WI sing 32 n n C15 C17 4WI sing 33 n n C15 C16 4WI sing 34 n n C18 C20 4WI sing 35 n n C18 C11 4WI sing 36 n n C10 C11 4WI sing 37 n n C3 H33 4WI sing 38 n n C6 H5 4WI sing 39 n n C6 H6 4WI sing 40 n n C7 H7 4WI sing 41 n n C7 H8 4WI sing 42 n n C10 H11 4WI sing 43 n n C10 H12 4WI sing 44 n n C5 H4 4WI sing 45 n n C9 H10 4WI sing 46 n n C11 H13 4WI sing 47 n n C12 H14 4WI sing 48 n n C19 H23 4WI sing 49 n n C19 H24 4WI sing 50 n n C19 H25 4WI sing 51 n n C20 H26 4WI sing 52 n n C20 H27 4WI sing 53 n n C20 H28 4WI sing 54 n n C16 H17 4WI sing 55 n n C16 H19 4WI sing 56 n n C16 H18 4WI sing 57 n n C17 H20 4WI sing 58 n n C17 H21 4WI sing 59 n n C17 H22 4WI sing 60 n n C23 H29 4WI sing 61 n n C23 H30 4WI sing 62 n n C23 H31 4WI sing 63 n n C4 H2 4WI sing 64 n n C4 H3 4WI sing 65 n n C2 H32 4WI sing 66 n n C14 H15 4WI sing 67 n n N5 H36 4WI sing 68 n n N2 H9 4WI sing 69 n n N1 H1 4WI sing 70 n n N4 H16 4WI sing 71 n n # _atom_sites.entry_id 9AVQ _atom_sites.fract_transf_matrix[1][1] 0.021863 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015499 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009507 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code B 2 4WI A 1 401 1 4WI 4WI . C 3 PEG A 1 402 2 PEG PEG . D 4 HOH A 1 501 13 HOH HOH . D 4 HOH A 2 502 5 HOH HOH . D 4 HOH A 3 503 10 HOH HOH . D 4 HOH A 4 504 2 HOH HOH . D 4 HOH A 5 505 15 HOH HOH . D 4 HOH A 6 506 12 HOH HOH . D 4 HOH A 7 507 11 HOH HOH . D 4 HOH A 8 508 3 HOH HOH . D 4 HOH A 9 509 14 HOH HOH . D 4 HOH A 10 510 9 HOH HOH . D 4 HOH A 11 511 8 HOH HOH . D 4 HOH A 12 512 6 HOH HOH . D 4 HOH A 13 513 1 HOH HOH . D 4 HOH A 14 514 7 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_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 _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C8 4WI . . . B 2 16.142 10.586 27.618 1 18.12 ? C8 4WI 401 A 1 HETATM 2 C C3 4WI . . . B 2 17.08 12.298 22.974 1 17.61 ? C3 4WI 401 A 1 HETATM 3 C C1 4WI . . . B 2 18.865 14.131 25.403 1 17.12 ? C1 4WI 401 A 1 HETATM 4 C C13 4WI . . . B 2 19.037 15.181 28.219 1 21.19 ? C13 4WI 401 A 1 HETATM 5 C C21 4WI . . . B 2 19.429 17.176 30.99 1 34.36 ? C21 4WI 401 A 1 HETATM 6 C C6 4WI . . . B 2 18.379 10.241 26.895 1 17.42 ? C6 4WI 401 A 1 HETATM 7 C C7 4WI . . . B 2 18.162 9.61 28.268 1 17.57 ? C7 4WI 401 A 1 HETATM 8 C C10 4WI . . . B 2 20.77 16.462 26.926 1 18.87 ? C10 4WI 401 A 1 HETATM 9 C C5 4WI . . . B 2 17.196 11.168 26.689 1 16.93 ? C5 4WI 401 A 1 HETATM 10 C C9 4WI . . . B 2 18.741 15.569 25.876 1 18.12 ? C9 4WI 401 A 1 HETATM 11 C C11 4WI . . . B 2 20.688 16.989 25.518 1 18.07 ? C11 4WI 401 A 1 HETATM 12 C C12 4WI . . . B 2 19.396 16.507 24.899 1 18.52 ? C12 4WI 401 A 1 HETATM 13 C C18 4WI . . . B 2 19.607 17.977 25.18 1 18.38 ? C18 4WI 401 A 1 HETATM 14 C C19 4WI . . . B 2 19.813 18.811 23.933 1 18.64 ? C19 4WI 401 A 1 HETATM 15 C C20 4WI . . . B 2 18.889 18.742 26.273 1 17.6 ? C20 4WI 401 A 1 HETATM 16 C C16 4WI . . . B 2 21.479 14.295 31.115 1 25.14 ? C16 4WI 401 A 1 HETATM 17 C C17 4WI . . . B 2 21.091 13.251 28.904 1 26.38 ? C17 4WI 401 A 1 HETATM 18 C C23 4WI . . . B 2 19.318 13.145 30.694 1 23.65 ? C23 4WI 401 A 1 HETATM 19 C C4 4WI . . . B 2 16.794 11.31 25.224 1 16.72 ? C4 4WI 401 A 1 HETATM 20 C C2 4WI . . . B 2 17.664 12.234 24.372 1 16.64 ? C2 4WI 401 A 1 HETATM 21 C C14 4WI . . . B 2 19.851 15.325 29.497 1 25.74 ? C14 4WI 401 A 1 HETATM 22 C C22 4WI . . . B 2 18.537 17.791 32.062 1 39.07 ? C22 4WI 401 A 1 HETATM 23 C C15 4WI . . . B 2 20.415 14.009 30.055 1 25.58 ? C15 4WI 401 A 1 HETATM 24 N N5 4WI . . . B 2 17.391 11.418 22.111 1 16.61 ? N5 4WI 401 A 1 HETATM 25 N N2 4WI . . . B 2 16.717 9.659 28.389 1 18.82 ? N2 4WI 401 A 1 HETATM 26 N N3 4WI . . . B 2 19.514 15.727 27.097 1 19.05 ? N3 4WI 401 A 1 HETATM 27 N N1 4WI . . . B 2 17.734 13.566 24.948 1 16.38 ? N1 4WI 401 A 1 HETATM 28 N N4 4WI . . . B 2 19.03 16.023 30.462 1 29.34 ? N4 4WI 401 A 1 HETATM 29 O O1 4WI . . . B 2 14.928 10.908 27.677 1 17.72 ? O1 4WI 401 A 1 HETATM 30 O O2 4WI . . . B 2 19.947 13.563 25.504 1 17.26 ? O2 4WI 401 A 1 HETATM 31 O O3 4WI . . . B 2 17.993 14.586 28.214 1 20.56 ? O3 4WI 401 A 1 HETATM 32 O O4 4WI . . . B 2 20.457 17.744 30.696 1 32.43 ? O4 4WI 401 A 1 HETATM 33 F F1 4WI . . . B 2 18.431 19.097 31.889 1 40.69 ? F1 4WI 401 A 1 HETATM 34 F F2 4WI . . . B 2 18.995 17.528 33.286 1 49.94 ? F2 4WI 401 A 1 HETATM 35 F F3 4WI . . . B 2 17.308 17.332 32.01 1 38.7 ? F3 4WI 401 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 35 #