data_8B2T # _model_server_result.job_id KkOWb-MI5-8AfynJwoqWrw _model_server_result.datetime_utc '2024-11-21 11:24:35' _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 8b2t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8B2T # _exptl.entry_id 8B2T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 500.554 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'Nirmatrelvir (reacted form)' _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 8B2T _cell.length_a 46.037 _cell.length_b 64.392 _cell.length_c 104.952 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8B2T _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 _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_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -64.392 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 C2 _struct_conn.ptnr2_label_comp_id OW1 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id OW1 _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 1.789 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C24 H35 F3 N4 O4' _chem_comp.formula_weight 500.554 _chem_comp.id OW1 _chem_comp.mon_nstd_flag . _chem_comp.name 'Nirmatrelvir (reacted form)' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms (1~{R},2~{S},5~{S})-3-[(2~{S})-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]-6,6-dimethyl-~{N}-[(2~{S})-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]but-3-en-2-yl]-3-azabicyclo[3.1.0]hexane-2-carboxamide # 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 C1 C2 OW1 doub 237 n n C2 C3 OW1 sing 238 n n C23 C22 OW1 sing 239 n n C3 N2 OW1 sing 240 n n C3 C4 OW1 sing 241 n n C11 C22 OW1 sing 242 n n C11 C12 OW1 sing 243 n n C11 C10 OW1 sing 244 n n N2 C9 OW1 sing 245 n n C22 C12 OW1 sing 246 n n C22 C24 OW1 sing 247 n n C4 C5 OW1 sing 248 n n C9 O2 OW1 doub 249 n n C9 C10 OW1 sing 250 n n C12 C13 OW1 sing 251 n n C10 N3 OW1 sing 252 n n C5 C6 OW1 sing 253 n n C5 C8 OW1 sing 254 n n C6 C7 OW1 sing 255 n n C13 N3 OW1 sing 256 n n N3 C14 OW1 sing 257 n n O1 C8 OW1 doub 258 n n C8 N1 OW1 sing 259 n n C7 N1 OW1 sing 260 n n O3 C14 OW1 doub 261 n n C14 C15 OW1 sing 262 n n C21 C18 OW1 sing 263 n n C15 C18 OW1 sing 264 n n C15 N4 OW1 sing 265 n n C18 C20 OW1 sing 266 n n C18 C19 OW1 sing 267 n n N4 C16 OW1 sing 268 n n O4 C16 OW1 doub 269 n n C16 C17 OW1 sing 270 n n F1 C17 OW1 sing 271 n n F2 C17 OW1 sing 272 n n C17 F3 OW1 sing 273 n n C1 H1 OW1 sing 274 n n C3 H4 OW1 sing 275 n n C4 H5 OW1 sing 276 n n C4 H6 OW1 sing 277 n n C5 H7 OW1 sing 278 n n C6 H8 OW1 sing 279 n n C6 H9 OW1 sing 280 n n C7 H10 OW1 sing 281 n n C7 H11 OW1 sing 282 n n N1 H12 OW1 sing 283 n n N2 H13 OW1 sing 284 n n C10 H14 OW1 sing 285 n n C11 H15 OW1 sing 286 n n C12 H16 OW1 sing 287 n n C13 H17 OW1 sing 288 n n C13 H18 OW1 sing 289 n n C15 H19 OW1 sing 290 n n N4 H20 OW1 sing 291 n n C19 H21 OW1 sing 292 n n C19 H22 OW1 sing 293 n n C19 H23 OW1 sing 294 n n C20 H24 OW1 sing 295 n n C20 H25 OW1 sing 296 n n C20 H26 OW1 sing 297 n n C21 H27 OW1 sing 298 n n C21 H28 OW1 sing 299 n n C21 H29 OW1 sing 300 n n C23 H30 OW1 sing 301 n n C23 H31 OW1 sing 302 n n C23 H32 OW1 sing 303 n n C24 H33 OW1 sing 304 n n C24 H34 OW1 sing 305 n n C24 H35 OW1 sing 306 n n C1 H2 OW1 sing 307 n n C2 H3 OW1 sing 308 n n # _atom_sites.entry_id 8B2T _atom_sites.fract_transf_matrix[1][1] 0.021722 _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] 0.01553 _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] 0.009528 _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 OW1 A 1 401 401 OW1 pro . C 3 HOH A 1 501 56 HOH HOH . C 3 HOH A 2 502 14 HOH HOH . C 3 HOH A 3 503 72 HOH HOH . C 3 HOH A 4 504 78 HOH HOH . C 3 HOH A 5 505 83 HOH HOH . C 3 HOH A 6 506 34 HOH HOH . C 3 HOH A 7 507 17 HOH HOH . C 3 HOH A 8 508 67 HOH HOH . C 3 HOH A 9 509 29 HOH HOH . C 3 HOH A 10 510 16 HOH HOH . C 3 HOH A 11 511 9 HOH HOH . C 3 HOH A 12 512 62 HOH HOH . C 3 HOH A 13 513 33 HOH HOH . C 3 HOH A 14 514 12 HOH HOH . C 3 HOH A 15 515 77 HOH HOH . C 3 HOH A 16 516 38 HOH HOH . C 3 HOH A 17 517 36 HOH HOH . C 3 HOH A 18 518 43 HOH HOH . C 3 HOH A 19 519 35 HOH HOH . C 3 HOH A 20 520 13 HOH HOH . C 3 HOH A 21 521 65 HOH HOH . C 3 HOH A 22 522 2 HOH HOH . C 3 HOH A 23 523 41 HOH HOH . C 3 HOH A 24 524 47 HOH HOH . C 3 HOH A 25 525 70 HOH HOH . C 3 HOH A 26 526 42 HOH HOH . C 3 HOH A 27 527 79 HOH HOH . C 3 HOH A 28 528 28 HOH HOH . C 3 HOH A 29 529 45 HOH HOH . C 3 HOH A 30 530 81 HOH HOH . C 3 HOH A 31 531 82 HOH HOH . C 3 HOH A 32 532 64 HOH HOH . C 3 HOH A 33 533 11 HOH HOH . C 3 HOH A 34 534 58 HOH HOH . C 3 HOH A 35 535 66 HOH HOH . C 3 HOH A 36 536 48 HOH HOH . C 3 HOH A 37 537 10 HOH HOH . C 3 HOH A 38 538 55 HOH HOH . C 3 HOH A 39 539 20 HOH HOH . C 3 HOH A 40 540 68 HOH HOH . C 3 HOH A 41 541 8 HOH HOH . C 3 HOH A 42 542 50 HOH HOH . C 3 HOH A 43 543 6 HOH HOH . C 3 HOH A 44 544 1 HOH HOH . C 3 HOH A 45 545 57 HOH HOH . C 3 HOH A 46 546 25 HOH HOH . C 3 HOH A 47 547 71 HOH HOH . C 3 HOH A 48 548 30 HOH HOH . C 3 HOH A 49 549 22 HOH HOH . C 3 HOH A 50 550 31 HOH HOH . C 3 HOH A 51 551 24 HOH HOH . C 3 HOH A 52 552 37 HOH HOH . C 3 HOH A 53 553 80 HOH HOH . C 3 HOH A 54 554 19 HOH HOH . C 3 HOH A 55 555 76 HOH HOH . C 3 HOH A 56 556 52 HOH HOH . C 3 HOH A 57 557 89 HOH HOH . C 3 HOH A 58 558 51 HOH HOH . C 3 HOH A 59 559 4 HOH HOH . C 3 HOH A 60 560 49 HOH HOH . C 3 HOH A 61 561 61 HOH HOH . C 3 HOH A 62 562 15 HOH HOH . C 3 HOH A 63 563 21 HOH HOH . C 3 HOH A 64 564 18 HOH HOH . C 3 HOH A 65 565 32 HOH HOH . C 3 HOH A 66 566 27 HOH HOH . C 3 HOH A 67 567 60 HOH HOH . C 3 HOH A 68 568 40 HOH HOH . C 3 HOH A 69 569 39 HOH HOH . C 3 HOH A 70 570 23 HOH HOH . C 3 HOH A 71 571 73 HOH HOH . C 3 HOH A 72 572 5 HOH HOH . C 3 HOH A 73 573 3 HOH HOH . C 3 HOH A 74 574 88 HOH HOH . C 3 HOH A 75 575 7 HOH HOH . C 3 HOH A 76 576 84 HOH HOH . C 3 HOH A 77 577 86 HOH HOH . C 3 HOH A 78 578 26 HOH HOH . C 3 HOH A 79 579 69 HOH HOH . C 3 HOH A 80 580 46 HOH HOH . C 3 HOH A 81 581 87 HOH HOH . C 3 HOH A 82 582 53 HOH HOH . C 3 HOH A 83 583 90 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 C1 OW1 . . . B 2 18.243 -20.591 -30.771 1 26.61 0 C1 OW1 401 A 1 HETATM 2 C C2 OW1 . . . B 2 17.576 -19.97 -29.811 1 26.92 0 C2 OW1 401 A 1 HETATM 3 C C3 OW1 . . . B 2 18.028 -19.937 -28.359 1 27 0 C3 OW1 401 A 1 HETATM 4 C C4 OW1 . . . B 2 17.035 -20.763 -27.536 1 24.36 0 C4 OW1 401 A 1 HETATM 5 C C5 OW1 . . . B 2 17.449 -20.966 -26.071 1 26.09 0 C5 OW1 401 A 1 HETATM 6 C C6 OW1 . . . B 2 18.692 -21.814 -25.802 1 23.14 0 C6 OW1 401 A 1 HETATM 7 C C7 OW1 . . . B 2 18.379 -22.631 -24.562 1 21.15 0 C7 OW1 401 A 1 HETATM 8 N N1 OW1 . . . B 2 16.927 -22.603 -24.505 1 23.29 0 N1 OW1 401 A 1 HETATM 9 C C8 OW1 . . . B 2 16.366 -21.668 -25.279 1 24.78 0 C8 OW1 401 A 1 HETATM 10 O O1 OW1 . . . B 2 15.169 -21.4 -25.338 1 22.09 0 O1 OW1 401 A 1 HETATM 11 N N2 OW1 . . . B 2 18.124 -18.571 -27.854 1 20.44 0 N2 OW1 401 A 1 HETATM 12 C C9 OW1 . . . B 2 19.252 -18.031 -27.384 1 23.4 0 C9 OW1 401 A 1 HETATM 13 O O2 OW1 . . . B 2 20.307 -18.653 -27.304 1 25.83 0 O2 OW1 401 A 1 HETATM 14 C C10 OW1 . . . B 2 19.157 -16.579 -26.91 1 22.46 0 C10 OW1 401 A 1 HETATM 15 C C11 OW1 . . . B 2 19.888 -15.642 -27.865 1 24.15 0 C11 OW1 401 A 1 HETATM 16 C C12 OW1 . . . B 2 21.1 -15.089 -27.139 1 24.78 0 C12 OW1 401 A 1 HETATM 17 C C13 OW1 . . . B 2 21.104 -15.655 -25.73 1 26.93 0 C13 OW1 401 A 1 HETATM 18 N N3 OW1 . . . B 2 19.846 -16.415 -25.628 1 23.05 0 N3 OW1 401 A 1 HETATM 19 C C14 OW1 . . . B 2 19.33 -16.943 -24.5 1 20.53 0 C14 OW1 401 A 1 HETATM 20 O O3 OW1 . . . B 2 18.26 -17.541 -24.504 1 22.59 0 O3 OW1 401 A 1 HETATM 21 C C15 OW1 . . . B 2 20.072 -16.736 -23.181 1 21.95 0 C15 OW1 401 A 1 HETATM 22 N N4 OW1 . . . B 2 19.179 -16.065 -22.249 1 19.41 0 N4 OW1 401 A 1 HETATM 23 C C16 OW1 . . . B 2 19.446 -14.854 -21.785 1 30.9 0 C16 OW1 401 A 1 HETATM 24 O O4 OW1 . . . B 2 20.431 -14.213 -22.088 1 34.83 0 O4 OW1 401 A 1 HETATM 25 C C17 OW1 . . . B 2 18.458 -14.255 -20.784 1 34.7 0 C17 OW1 401 A 1 HETATM 26 F F1 OW1 . . . B 2 17.199 -14.597 -21.01 1 46.35 0 F1 OW1 401 A 1 HETATM 27 F F2 OW1 . . . B 2 18.495 -12.932 -20.833 1 44 0 F2 OW1 401 A 1 HETATM 28 F F3 OW1 . . . B 2 18.744 -14.649 -19.553 1 50.16 0 F3 OW1 401 A 1 HETATM 29 C C18 OW1 . . . B 2 20.669 -18.036 -22.594 1 21.31 0 C18 OW1 401 A 1 HETATM 30 C C19 OW1 . . . B 2 21.456 -17.688 -21.328 1 24.17 0 C19 OW1 401 A 1 HETATM 31 C C20 OW1 . . . B 2 19.607 -19.077 -22.22 1 20.21 0 C20 OW1 401 A 1 HETATM 32 C C21 OW1 . . . B 2 21.615 -18.656 -23.62 1 25.05 0 C21 OW1 401 A 1 HETATM 33 C C22 OW1 . . . B 2 20.002 -14.165 -27.572 1 31.33 0 C22 OW1 401 A 1 HETATM 34 C C23 OW1 . . . B 2 20.366 -13.235 -28.712 1 28.85 0 C23 OW1 401 A 1 HETATM 35 C C24 OW1 . . . B 2 19.027 -13.544 -26.593 1 27.44 0 C24 OW1 401 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 35 #