data_6XJ8 # _model_server_result.job_id GVVdQ_nR-qdaC38uafl-hQ _model_server_result.datetime_utc '2024-11-12 23:39:45' _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 6xj8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 6XJ8 # _exptl.entry_id 6XJ8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 317.361 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1H-pyrrole -5-carboxylic acid' _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 6XJ8 _cell.length_a 56.599 _cell.length_b 59.36 _cell.length_c 77.62 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XJ8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 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 disulf _struct_conn.details ? _struct_conn.id disulf1 _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 68 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 69 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 237 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 238 _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 2.056 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C12 H19 N3 O5 S' _chem_comp.formula_weight 317.361 _chem_comp.id 8YF _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1H-pyrrole -5-carboxylic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Imipenem, hydrolyzed 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 N26 C25 8YF doub 1 n n C25 N24 8YF sing 2 n n N24 C23 8YF sing 3 n n C23 C22 8YF sing 4 n n C22 S21 8YF sing 5 n n O31 C31 8YF doub 6 n n O32 C31 8YF sing 7 n n S21 C2 8YF sing 8 n n C31 C3 8YF sing 9 n n C3 C2 8YF doub 10 n n C3 N4 8YF sing 11 n n C2 C1 8YF sing 12 n n N4 C5 8YF sing 13 n n C1 C5 8YF sing 14 n n C5 C6 8YF sing 15 n n O71 C7 8YF doub 16 n n C7 C6 8YF sing 17 n n C7 O72 8YF sing 18 n n C6 C61 8YF sing 19 n n C61 C62 8YF sing 20 n n C61 O62 8YF sing 21 n n C62 H1 8YF sing 22 n n C62 H2 8YF sing 23 n n C62 H3 8YF sing 24 n n C61 H4 8YF sing 25 n n O62 H5 8YF sing 26 n n C6 H6 8YF sing 27 n n O72 H7 8YF sing 28 n n C5 H8 8YF sing 29 n n C1 H9 8YF sing 30 n n C1 H10 8YF sing 31 n n N4 H11 8YF sing 32 n n O32 H12 8YF sing 33 n n C22 H13 8YF sing 34 n n C22 H14 8YF sing 35 n n C23 H15 8YF sing 36 n n C23 H16 8YF sing 37 n n C25 H17 8YF sing 38 n n N26 H18 8YF sing 39 n n N24 H20 8YF sing 40 n n # _atom_sites.entry_id 6XJ8 _atom_sites.fract_transf_matrix[1][1] 0.017668 _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] 0.016846 _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] 0.012883 _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 8YF A 1 301 301 8YF 8YF . C 3 HOH A 1 401 24 HOH HOH . C 3 HOH A 2 402 27 HOH HOH . C 3 HOH A 3 403 20 HOH HOH . C 3 HOH A 4 404 48 HOH HOH . C 3 HOH A 5 405 1 HOH HOH . C 3 HOH A 6 406 31 HOH HOH . C 3 HOH A 7 407 85 HOH HOH . C 3 HOH A 8 408 14 HOH HOH . C 3 HOH A 9 409 115 HOH HOH . C 3 HOH A 10 410 37 HOH HOH . C 3 HOH A 11 411 35 HOH HOH . C 3 HOH A 12 412 63 HOH HOH . C 3 HOH A 13 413 9 HOH HOH . C 3 HOH A 14 414 7 HOH HOH . C 3 HOH A 15 415 94 HOH HOH . C 3 HOH A 16 416 45 HOH HOH . C 3 HOH A 17 417 58 HOH HOH . C 3 HOH A 18 418 62 HOH HOH . C 3 HOH A 19 419 122 HOH HOH . C 3 HOH A 20 420 135 HOH HOH . C 3 HOH A 21 421 41 HOH HOH . C 3 HOH A 22 422 3 HOH HOH . C 3 HOH A 23 423 123 HOH HOH . C 3 HOH A 24 424 13 HOH HOH . C 3 HOH A 25 425 28 HOH HOH . C 3 HOH A 26 426 90 HOH HOH . C 3 HOH A 27 427 49 HOH HOH . C 3 HOH A 28 428 38 HOH HOH . C 3 HOH A 29 429 86 HOH HOH . C 3 HOH A 30 430 12 HOH HOH . C 3 HOH A 31 431 72 HOH HOH . C 3 HOH A 32 432 133 HOH HOH . C 3 HOH A 33 433 128 HOH HOH . C 3 HOH A 34 434 88 HOH HOH . C 3 HOH A 35 435 19 HOH HOH . C 3 HOH A 36 436 103 HOH HOH . C 3 HOH A 37 437 68 HOH HOH . C 3 HOH A 38 438 30 HOH HOH . C 3 HOH A 39 439 67 HOH HOH . C 3 HOH A 40 440 77 HOH HOH . C 3 HOH A 41 441 84 HOH HOH . C 3 HOH A 42 442 50 HOH HOH . C 3 HOH A 43 443 4 HOH HOH . C 3 HOH A 44 444 125 HOH HOH . C 3 HOH A 45 445 26 HOH HOH . C 3 HOH A 46 446 39 HOH HOH . C 3 HOH A 47 447 119 HOH HOH . C 3 HOH A 48 448 105 HOH HOH . C 3 HOH A 49 449 2 HOH HOH . C 3 HOH A 50 450 36 HOH HOH . C 3 HOH A 51 451 21 HOH HOH . C 3 HOH A 52 452 80 HOH HOH . C 3 HOH A 53 453 139 HOH HOH . C 3 HOH A 54 454 73 HOH HOH . C 3 HOH A 55 455 22 HOH HOH . C 3 HOH A 56 456 75 HOH HOH . C 3 HOH A 57 457 17 HOH HOH . C 3 HOH A 58 458 5 HOH HOH . C 3 HOH A 59 459 53 HOH HOH . C 3 HOH A 60 460 55 HOH HOH . C 3 HOH A 61 461 11 HOH HOH . C 3 HOH A 62 462 95 HOH HOH . C 3 HOH A 63 463 61 HOH HOH . C 3 HOH A 64 464 8 HOH HOH . C 3 HOH A 65 465 60 HOH HOH . C 3 HOH A 66 466 137 HOH HOH . C 3 HOH A 67 467 112 HOH HOH . C 3 HOH A 68 468 144 HOH HOH . C 3 HOH A 69 469 42 HOH HOH . C 3 HOH A 70 470 10 HOH HOH . C 3 HOH A 71 471 32 HOH HOH . C 3 HOH A 72 472 52 HOH HOH . C 3 HOH A 73 473 29 HOH HOH . C 3 HOH A 74 474 129 HOH HOH . C 3 HOH A 75 475 81 HOH HOH . C 3 HOH A 76 476 54 HOH HOH . C 3 HOH A 77 477 47 HOH HOH . C 3 HOH A 78 478 43 HOH HOH . C 3 HOH A 79 479 25 HOH HOH . C 3 HOH A 80 480 74 HOH HOH . C 3 HOH A 81 481 69 HOH HOH . C 3 HOH A 82 482 111 HOH HOH . C 3 HOH A 83 483 23 HOH HOH . C 3 HOH A 84 484 136 HOH HOH . C 3 HOH A 85 485 15 HOH HOH . C 3 HOH A 86 486 33 HOH HOH . C 3 HOH A 87 487 40 HOH HOH . C 3 HOH A 88 488 59 HOH HOH . C 3 HOH A 89 489 51 HOH HOH . C 3 HOH A 90 490 87 HOH HOH . C 3 HOH A 91 491 117 HOH HOH . C 3 HOH A 92 492 79 HOH HOH . C 3 HOH A 93 493 34 HOH HOH . C 3 HOH A 94 494 143 HOH HOH . C 3 HOH A 95 495 116 HOH HOH . C 3 HOH A 96 496 64 HOH HOH . C 3 HOH A 97 497 91 HOH HOH . C 3 HOH A 98 498 78 HOH HOH . C 3 HOH A 99 499 124 HOH HOH . C 3 HOH A 100 500 106 HOH HOH . C 3 HOH A 101 501 104 HOH HOH . C 3 HOH A 102 502 100 HOH HOH . C 3 HOH A 103 503 18 HOH HOH . C 3 HOH A 104 504 89 HOH HOH . C 3 HOH A 105 505 121 HOH HOH . C 3 HOH A 106 506 98 HOH HOH . C 3 HOH A 107 507 149 HOH HOH . C 3 HOH A 108 508 150 HOH HOH . C 3 HOH A 109 509 114 HOH HOH . C 3 HOH A 110 510 109 HOH HOH . C 3 HOH A 111 511 93 HOH HOH . C 3 HOH A 112 512 108 HOH HOH . C 3 HOH A 113 513 44 HOH HOH . C 3 HOH A 114 514 113 HOH HOH . C 3 HOH A 115 515 147 HOH HOH . C 3 HOH A 116 516 102 HOH HOH . C 3 HOH A 117 517 71 HOH HOH . C 3 HOH A 118 518 57 HOH HOH . C 3 HOH A 119 519 126 HOH HOH . C 3 HOH A 120 520 142 HOH HOH . C 3 HOH A 121 521 97 HOH HOH . C 3 HOH A 122 522 16 HOH HOH . C 3 HOH A 123 523 134 HOH HOH . C 3 HOH A 124 524 92 HOH HOH . C 3 HOH A 125 525 131 HOH HOH . C 3 HOH A 126 526 145 HOH HOH . C 3 HOH A 127 527 130 HOH HOH . C 3 HOH A 128 528 82 HOH HOH . C 3 HOH A 129 529 107 HOH HOH . C 3 HOH A 130 530 46 HOH HOH . C 3 HOH A 131 531 120 HOH HOH . C 3 HOH A 132 532 141 HOH HOH . C 3 HOH A 133 533 146 HOH HOH . C 3 HOH A 134 534 65 HOH HOH . C 3 HOH A 135 535 70 HOH HOH . C 3 HOH A 136 536 56 HOH HOH . C 3 HOH A 137 537 99 HOH HOH . C 3 HOH A 138 538 96 HOH HOH . C 3 HOH A 139 539 6 HOH HOH . C 3 HOH A 140 540 132 HOH HOH . C 3 HOH A 141 541 138 HOH HOH . C 3 HOH A 142 542 118 HOH HOH . C 3 HOH A 143 543 101 HOH HOH . C 3 HOH A 144 544 110 HOH HOH . C 3 HOH A 145 545 76 HOH HOH . C 3 HOH A 146 546 148 HOH HOH . C 3 HOH A 147 547 66 HOH HOH . C 3 HOH A 148 548 83 HOH HOH . C 3 HOH A 149 549 127 HOH HOH . C 3 HOH A 150 550 140 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 C62 8YF . . . B 2 23.644 14.312 6.764 0.79 34.97 ? C62 8YF 301 A 1 HETATM 2 C C61 8YF . . . B 2 23.082 13.586 7.975 0.79 34.98 ? C61 8YF 301 A 1 HETATM 3 O O62 8YF . . . B 2 24.023 13.555 8.996 0.79 35.86 ? O62 8YF 301 A 1 HETATM 4 C C6 8YF . . . B 2 21.784 14.261 8.529 0.79 32 ? C6 8YF 301 A 1 HETATM 5 C C7 8YF . . . B 2 21.031 13.139 9.33 0.79 32.09 ? C7 8YF 301 A 1 HETATM 6 O O71 8YF . . . B 2 21.551 11.991 9.415 0.79 41.43 -1 O71 8YF 301 A 1 HETATM 7 O O72 8YF . . . B 2 19.932 13.371 9.906 0.79 29.02 ? O72 8YF 301 A 1 HETATM 8 C C5 8YF . . . B 2 22.143 15.404 9.514 0.79 24.92 ? C5 8YF 301 A 1 HETATM 9 C C1 8YF . . . B 2 22.335 16.758 8.815 0.79 30.15 ? C1 8YF 301 A 1 HETATM 10 N N4 8YF . . . B 2 21.01 15.646 10.421 0.79 25.94 ? N4 8YF 301 A 1 HETATM 11 C C3 8YF . . . B 2 20.212 16.521 9.793 0.79 21.85 ? C3 8YF 301 A 1 HETATM 12 C C31 8YF . . . B 2 19.018 17.163 10.488 0.79 24.49 ? C31 8YF 301 A 1 HETATM 13 O O31 8YF . . . B 2 18.07 17.612 9.796 0.79 26.08 -1 O31 8YF 301 A 1 HETATM 14 O O32 8YF . . . B 2 18.972 17.259 11.742 0.79 24.91 ? O32 8YF 301 A 1 HETATM 15 C C2 8YF . . . B 2 21.142 17.384 9.006 0.79 34.84 ? C2 8YF 301 A 1 HETATM 16 S S21 8YF . . . B 2 20.464 18.507 7.756 0.79 62.5 ? S21 8YF 301 A 1 HETATM 17 C C22 8YF . . . B 2 20.024 20.001 8.7 0.79 44.3 ? C22 8YF 301 A 1 HETATM 18 C C23 8YF . . . B 2 19.488 21.073 7.752 0.79 45.63 ? C23 8YF 301 A 1 HETATM 19 N N24 8YF . . . B 2 18.586 22.029 8.388 0.79 56.31 ? N24 8YF 301 A 1 HETATM 20 C C25 8YF . . . B 2 18.168 23.123 7.718 0.79 51.07 ? C25 8YF 301 A 1 HETATM 21 N N26 8YF . . . B 2 17.393 23.956 8.252 0.79 41.36 ? N26 8YF 301 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 208 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #