data_6YD5 # _model_server_result.job_id uekGB073eQcMFNFO39ocZg _model_server_result.datetime_utc '2025-07-12 23:27:29' _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 6yd5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 6YD5 # _exptl.entry_id 6YD5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 99.131 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-methylpyrrolidin-2-one _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 111.49 _cell.angle_gamma 90 _cell.entry_id 6YD5 _cell.length_a 72.404 _cell.length_b 50.182 _cell.length_c 88.6 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YD5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _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,D,E,F,G _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 A O LEU 192 A LEU 200 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc2 A O VAL 195 A VAL 203 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc3 A OD1 ASN 200 A ASN 208 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc4 A O LEU 201 A LEU 209 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? metalc ? metalc5 D K K . A K 403 1_555 E O OM8 . A OM8 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? # _chem_comp.formula 'C5 H9 N O' _chem_comp.formula_weight 99.131 _chem_comp.id MB3 _chem_comp.mon_nstd_flag . _chem_comp.name 1-methylpyrrolidin-2-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 CAA NAG MB3 sing 259 n n CAA HAA MB3 sing 260 n n CAA HAAA MB3 sing 261 n n CAA HAAB MB3 sing 262 n n CAF OAB MB3 doub 263 n n CAE CAC MB3 sing 264 n n CAC CAD MB3 sing 265 n n CAC HAC MB3 sing 266 n n CAC HACA MB3 sing 267 n n CAF CAD MB3 sing 268 n n CAD HAD MB3 sing 269 n n CAD HADA MB3 sing 270 n n NAG CAE MB3 sing 271 n n CAE HAE MB3 sing 272 n n CAE HAEA MB3 sing 273 n n NAG CAF MB3 sing 274 n n # _atom_sites.entry_id 6YD5 _atom_sites.fract_transf_matrix[1][1] 0.013811 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005438 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019927 _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] 0.01213 _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 GDP A 1 401 1 GDP GDP . C 3 MB3 A 1 402 1 MB3 MB3 . D 4 K A 1 403 1 K K . E 5 OM8 A 1 404 1 OM8 9PX . F 6 EDO A 1 405 1 EDO EDO . G 7 HOH A 1 501 207 HOH HOH . G 7 HOH A 2 502 220 HOH HOH . G 7 HOH A 3 503 224 HOH HOH . G 7 HOH A 4 504 125 HOH HOH . G 7 HOH A 5 505 222 HOH HOH . G 7 HOH A 6 506 177 HOH HOH . G 7 HOH A 7 507 128 HOH HOH . G 7 HOH A 8 508 181 HOH HOH . G 7 HOH A 9 509 83 HOH HOH . G 7 HOH A 10 510 154 HOH HOH . G 7 HOH A 11 511 188 HOH HOH . G 7 HOH A 12 512 15 HOH HOH . G 7 HOH A 13 513 208 HOH HOH . G 7 HOH A 14 514 182 HOH HOH . G 7 HOH A 15 515 185 HOH HOH . G 7 HOH A 16 516 218 HOH HOH . G 7 HOH A 17 517 54 HOH HOH . G 7 HOH A 18 518 202 HOH HOH . G 7 HOH A 19 519 150 HOH HOH . G 7 HOH A 20 520 200 HOH HOH . G 7 HOH A 21 521 131 HOH HOH . G 7 HOH A 22 522 18 HOH HOH . G 7 HOH A 23 523 190 HOH HOH . G 7 HOH A 24 524 216 HOH HOH . G 7 HOH A 25 525 42 HOH HOH . G 7 HOH A 26 526 27 HOH HOH . G 7 HOH A 27 527 75 HOH HOH . G 7 HOH A 28 528 192 HOH HOH . G 7 HOH A 29 529 102 HOH HOH . G 7 HOH A 30 530 43 HOH HOH . G 7 HOH A 31 531 215 HOH HOH . G 7 HOH A 32 532 37 HOH HOH . G 7 HOH A 33 533 95 HOH HOH . G 7 HOH A 34 534 21 HOH HOH . G 7 HOH A 35 535 96 HOH HOH . G 7 HOH A 36 536 47 HOH HOH . G 7 HOH A 37 537 126 HOH HOH . G 7 HOH A 38 538 30 HOH HOH . G 7 HOH A 39 539 178 HOH HOH . G 7 HOH A 40 540 5 HOH HOH . G 7 HOH A 41 541 36 HOH HOH . G 7 HOH A 42 542 35 HOH HOH . G 7 HOH A 43 543 52 HOH HOH . G 7 HOH A 44 544 99 HOH HOH . G 7 HOH A 45 545 41 HOH HOH . G 7 HOH A 46 546 189 HOH HOH . G 7 HOH A 47 547 46 HOH HOH . G 7 HOH A 48 548 103 HOH HOH . G 7 HOH A 49 549 133 HOH HOH . G 7 HOH A 50 550 32 HOH HOH . G 7 HOH A 51 551 82 HOH HOH . G 7 HOH A 52 552 145 HOH HOH . G 7 HOH A 53 553 53 HOH HOH . G 7 HOH A 54 554 92 HOH HOH . G 7 HOH A 55 555 56 HOH HOH . G 7 HOH A 56 556 187 HOH HOH . G 7 HOH A 57 557 10 HOH HOH . G 7 HOH A 58 558 6 HOH HOH . G 7 HOH A 59 559 88 HOH HOH . G 7 HOH A 60 560 69 HOH HOH . G 7 HOH A 61 561 89 HOH HOH . G 7 HOH A 62 562 144 HOH HOH . G 7 HOH A 63 563 138 HOH HOH . G 7 HOH A 64 564 3 HOH HOH . G 7 HOH A 65 565 9 HOH HOH . G 7 HOH A 66 566 86 HOH HOH . G 7 HOH A 67 567 62 HOH HOH . G 7 HOH A 68 568 94 HOH HOH . G 7 HOH A 69 569 196 HOH HOH . G 7 HOH A 70 570 44 HOH HOH . G 7 HOH A 71 571 212 HOH HOH . G 7 HOH A 72 572 33 HOH HOH . G 7 HOH A 73 573 87 HOH HOH . G 7 HOH A 74 574 38 HOH HOH . G 7 HOH A 75 575 204 HOH HOH . G 7 HOH A 76 576 14 HOH HOH . G 7 HOH A 77 577 113 HOH HOH . G 7 HOH A 78 578 16 HOH HOH . G 7 HOH A 79 579 23 HOH HOH . G 7 HOH A 80 580 22 HOH HOH . G 7 HOH A 81 581 217 HOH HOH . G 7 HOH A 82 582 1 HOH HOH . G 7 HOH A 83 583 104 HOH HOH . G 7 HOH A 84 584 24 HOH HOH . G 7 HOH A 85 585 195 HOH HOH . G 7 HOH A 86 586 223 HOH HOH . G 7 HOH A 87 587 81 HOH HOH . G 7 HOH A 88 588 60 HOH HOH . G 7 HOH A 89 589 183 HOH HOH . G 7 HOH A 90 590 28 HOH HOH . G 7 HOH A 91 591 51 HOH HOH . G 7 HOH A 92 592 119 HOH HOH . G 7 HOH A 93 593 221 HOH HOH . G 7 HOH A 94 594 17 HOH HOH . G 7 HOH A 95 595 129 HOH HOH . G 7 HOH A 96 596 74 HOH HOH . G 7 HOH A 97 597 39 HOH HOH . G 7 HOH A 98 598 70 HOH HOH . G 7 HOH A 99 599 55 HOH HOH . G 7 HOH A 100 600 7 HOH HOH . G 7 HOH A 101 601 84 HOH HOH . G 7 HOH A 102 602 146 HOH HOH . G 7 HOH A 103 603 143 HOH HOH . G 7 HOH A 104 604 151 HOH HOH . G 7 HOH A 105 605 8 HOH HOH . G 7 HOH A 106 606 109 HOH HOH . G 7 HOH A 107 607 127 HOH HOH . G 7 HOH A 108 608 2 HOH HOH . G 7 HOH A 109 609 31 HOH HOH . G 7 HOH A 110 610 34 HOH HOH . G 7 HOH A 111 611 68 HOH HOH . G 7 HOH A 112 612 101 HOH HOH . G 7 HOH A 113 613 4 HOH HOH . G 7 HOH A 114 614 67 HOH HOH . G 7 HOH A 115 615 49 HOH HOH . G 7 HOH A 116 616 25 HOH HOH . G 7 HOH A 117 617 13 HOH HOH . G 7 HOH A 118 618 209 HOH HOH . G 7 HOH A 119 619 134 HOH HOH . G 7 HOH A 120 620 11 HOH HOH . G 7 HOH A 121 621 29 HOH HOH . G 7 HOH A 122 622 26 HOH HOH . G 7 HOH A 123 623 137 HOH HOH . G 7 HOH A 124 624 64 HOH HOH . G 7 HOH A 125 625 79 HOH HOH . G 7 HOH A 126 626 66 HOH HOH . G 7 HOH A 127 627 58 HOH HOH . G 7 HOH A 128 628 213 HOH HOH . G 7 HOH A 129 629 180 HOH HOH . G 7 HOH A 130 630 85 HOH HOH . G 7 HOH A 131 631 12 HOH HOH . G 7 HOH A 132 632 116 HOH HOH . G 7 HOH A 133 633 108 HOH HOH . G 7 HOH A 134 634 159 HOH HOH . G 7 HOH A 135 635 40 HOH HOH . G 7 HOH A 136 636 112 HOH HOH . G 7 HOH A 137 637 93 HOH HOH . G 7 HOH A 138 638 169 HOH HOH . G 7 HOH A 139 639 98 HOH HOH . G 7 HOH A 140 640 77 HOH HOH . G 7 HOH A 141 641 155 HOH HOH . G 7 HOH A 142 642 71 HOH HOH . G 7 HOH A 143 643 142 HOH HOH . G 7 HOH A 144 644 118 HOH HOH . G 7 HOH A 145 645 19 HOH HOH . G 7 HOH A 146 646 114 HOH HOH . G 7 HOH A 147 647 65 HOH HOH . G 7 HOH A 148 648 130 HOH HOH . G 7 HOH A 149 649 97 HOH HOH . G 7 HOH A 150 650 110 HOH HOH . G 7 HOH A 151 651 193 HOH HOH . G 7 HOH A 152 652 20 HOH HOH . G 7 HOH A 153 653 121 HOH HOH . G 7 HOH A 154 654 59 HOH HOH . G 7 HOH A 155 655 80 HOH HOH . G 7 HOH A 156 656 61 HOH HOH . G 7 HOH A 157 657 205 HOH HOH . G 7 HOH A 158 658 57 HOH HOH . G 7 HOH A 159 659 206 HOH HOH . G 7 HOH A 160 660 115 HOH HOH . G 7 HOH A 161 661 160 HOH HOH . G 7 HOH A 162 662 73 HOH HOH . G 7 HOH A 163 663 148 HOH HOH . G 7 HOH A 164 664 107 HOH HOH . G 7 HOH A 165 665 214 HOH HOH . G 7 HOH A 166 666 166 HOH HOH . G 7 HOH A 167 667 198 HOH HOH . G 7 HOH A 168 668 63 HOH HOH . G 7 HOH A 169 669 50 HOH HOH . G 7 HOH A 170 670 123 HOH HOH . G 7 HOH A 171 671 179 HOH HOH . G 7 HOH A 172 672 152 HOH HOH . G 7 HOH A 173 673 100 HOH HOH . G 7 HOH A 174 674 106 HOH HOH . G 7 HOH A 175 675 167 HOH HOH . G 7 HOH A 176 676 201 HOH HOH . G 7 HOH A 177 677 91 HOH HOH . G 7 HOH A 178 678 147 HOH HOH . G 7 HOH A 179 679 203 HOH HOH . G 7 HOH A 180 680 211 HOH HOH . G 7 HOH A 181 681 136 HOH HOH . G 7 HOH A 182 682 176 HOH HOH . G 7 HOH A 183 683 199 HOH HOH . G 7 HOH A 184 684 72 HOH HOH . G 7 HOH A 185 685 175 HOH HOH . G 7 HOH A 186 686 163 HOH HOH . G 7 HOH A 187 687 172 HOH HOH . G 7 HOH A 188 688 161 HOH HOH . G 7 HOH A 189 689 124 HOH HOH . G 7 HOH A 190 690 162 HOH HOH . G 7 HOH A 191 691 174 HOH HOH . G 7 HOH A 192 692 48 HOH HOH . G 7 HOH A 193 693 45 HOH HOH . G 7 HOH A 194 694 168 HOH HOH . G 7 HOH A 195 695 184 HOH HOH . G 7 HOH A 196 696 197 HOH HOH . G 7 HOH A 197 697 191 HOH HOH . G 7 HOH A 198 698 139 HOH HOH . G 7 HOH A 199 699 225 HOH HOH . G 7 HOH A 200 700 149 HOH HOH . G 7 HOH A 201 701 165 HOH HOH . G 7 HOH A 202 702 173 HOH HOH . G 7 HOH A 203 703 132 HOH HOH . G 7 HOH A 204 704 158 HOH HOH . G 7 HOH A 205 705 76 HOH HOH . G 7 HOH A 206 706 111 HOH HOH . G 7 HOH A 207 707 78 HOH HOH . G 7 HOH A 208 708 140 HOH HOH . G 7 HOH A 209 709 164 HOH HOH . G 7 HOH A 210 710 122 HOH HOH . G 7 HOH A 211 711 90 HOH HOH . G 7 HOH A 212 712 105 HOH HOH . G 7 HOH A 213 713 135 HOH HOH . G 7 HOH A 214 714 210 HOH HOH . G 7 HOH A 215 715 170 HOH HOH . G 7 HOH A 216 716 156 HOH HOH . G 7 HOH A 217 717 219 HOH HOH . G 7 HOH A 218 718 141 HOH HOH . G 7 HOH A 219 719 194 HOH HOH . G 7 HOH A 220 720 153 HOH HOH . G 7 HOH A 221 721 117 HOH HOH . G 7 HOH A 222 722 186 HOH HOH . G 7 HOH A 223 723 171 HOH HOH . G 7 HOH A 224 724 120 HOH HOH . G 7 HOH A 225 725 157 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 CAA MB3 . . . C 3 -3.297 -3.078 20.561 1 29.37 ? CAA MB3 402 A 1 HETATM 2 O OAB MB3 . . . C 3 -0.881 -3.291 18.844 1 30.35 ? OAB MB3 402 A 1 HETATM 3 C CAC MB3 . . . C 3 -0.521 -5.476 21.639 1 29.56 ? CAC MB3 402 A 1 HETATM 4 C CAD MB3 . . . C 3 0.12 -4.79 20.436 1 29.45 ? CAD MB3 402 A 1 HETATM 5 C CAE MB3 . . . C 3 -1.802 -4.691 21.919 1 29.41 ? CAE MB3 402 A 1 HETATM 6 C CAF MB3 . . . C 3 -0.951 -3.881 19.866 1 29.23 ? CAF MB3 402 A 1 HETATM 7 N NAG MB3 . . . C 3 -2.078 -3.842 20.771 1 28.93 ? NAG MB3 402 A 1 HETATM 8 H HAA MB3 . . . C 3 -3.976 -3.375 21.187 1 35.25 ? HAA MB3 402 A 1 HETATM 9 H HAAA MB3 . . . C 3 -3.611 -3.215 19.653 1 35.25 ? HAAA MB3 402 A 1 HETATM 10 H HAAB MB3 . . . C 3 -3.116 -2.136 20.702 1 35.25 ? HAAB MB3 402 A 1 HETATM 11 H HAC MB3 . . . C 3 -0.736 -6.396 21.422 1 35.47 ? HAC MB3 402 A 1 HETATM 12 H HACA MB3 . . . C 3 0.072 -5.428 22.405 1 35.47 ? HACA MB3 402 A 1 HETATM 13 H HAD MB3 . . . C 3 0.886 -4.267 20.72 1 35.34 ? HAD MB3 402 A 1 HETATM 14 H HADA MB3 . . . C 3 0.382 -5.451 19.776 1 35.34 ? HADA MB3 402 A 1 HETATM 15 H HAE MB3 . . . C 3 -2.539 -5.308 22.05 1 35.29 ? HAE MB3 402 A 1 HETATM 16 H HAEA MB3 . . . C 3 -1.679 -4.139 22.707 1 35.29 ? HAEA MB3 402 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 16 #