data_4KQ5 # _model_server_result.job_id SdhYVmwmheJnF1twzBpnKA _model_server_result.datetime_utc '2024-11-05 23:19:56' _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 4kq5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":404}' # _entry.id 4KQ5 # _exptl.entry_id 4KQ5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 272.09 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ZOLEDRONIC 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 4KQ5 _cell.length_a 111.65 _cell.length_b 111.65 _cell.length_c 67.94 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KQ5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 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,E,F,G _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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _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 OD2 ASP 125 A ASP 103 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc2 A OD1 ASP 125 A ASP 103 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc3 A OD2 ASP 129 A ASP 107 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc4 A OD2 ASP 129 A ASP 107 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc5 A OD2 ASP 265 A ASP 243 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc6 B MG MG . A MG 401 1_555 E O17 ZOL . A ZOL 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc7 B MG MG . A MG 401 1_555 E O12 ZOL . A ZOL 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc8 B MG MG . A MG 401 1_555 G O HOH . A HOH 584 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc9 B MG MG . A MG 401 1_555 G O HOH . A HOH 585 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc10 C MG MG . A MG 402 1_555 E O11 ZOL . A ZOL 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc11 C MG MG . A MG 402 1_555 E O16 ZOL . A ZOL 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc12 C MG MG . A MG 402 1_555 G O HOH . A HOH 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc13 C MG MG . A MG 402 1_555 G O HOH . A HOH 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc14 C MG MG . A MG 402 1_555 G O HOH . A HOH 588 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc15 D MG MG . A MG 403 1_555 E O12 ZOL . A ZOL 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc16 D MG MG . A MG 403 1_555 G O HOH . A HOH 589 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc17 D MG MG . A MG 403 1_555 G O HOH . A HOH 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc18 D MG MG . A MG 403 1_555 G O HOH . A HOH 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? # _chem_comp.formula 'C5 H10 N2 O7 P2' _chem_comp.formula_weight 272.09 _chem_comp.id ZOL _chem_comp.mon_nstd_flag . _chem_comp.name 'ZOLEDRONIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID' # 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 O17 P14 ZOL sing 385 n n O17 H17 ZOL sing 386 n n P14 O16 ZOL sing 387 n n P14 O15 ZOL doub 388 n n P14 C8 ZOL sing 389 n n O16 H1 ZOL sing 390 n n C8 P9 ZOL sing 391 n n C8 O13 ZOL sing 392 n n C8 C7 ZOL sing 393 n n P9 O10 ZOL sing 394 n n P9 O11 ZOL sing 395 n n P9 O12 ZOL doub 396 n n O10 H10 ZOL sing 397 n n O11 H11 ZOL sing 398 n n O13 H13 ZOL sing 399 n n C7 N15 ZOL sing 400 n n C7 H71 ZOL sing 401 n n C7 H72 ZOL sing 402 n n N15 C16 ZOL sing 403 n y N15 C19 ZOL sing 404 n y C16 N17 ZOL doub 405 n y C16 H16 ZOL sing 406 n n N17 C18 ZOL sing 407 n y C18 C19 ZOL doub 408 n y C18 H18 ZOL sing 409 n n C19 H19 ZOL sing 410 n n # _atom_sites.entry_id 4KQ5 _atom_sites.fract_transf_matrix[1][1] 0.008957 _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] 0.008957 _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] 0.014719 _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 MG A 1 401 907 MG MG . C 2 MG A 1 402 908 MG MG . D 2 MG A 1 403 909 MG MG . E 3 ZOL A 1 404 901 ZOL ZOL . F 4 EDO A 1 405 1 EDO EDO . G 5 HOH A 1 501 1 HOH HOH . G 5 HOH A 2 502 2 HOH HOH . G 5 HOH A 3 503 3 HOH HOH . G 5 HOH A 4 504 4 HOH HOH . G 5 HOH A 5 505 5 HOH HOH . G 5 HOH A 6 506 6 HOH HOH . G 5 HOH A 7 507 7 HOH HOH . G 5 HOH A 8 508 8 HOH HOH . G 5 HOH A 9 509 9 HOH HOH . G 5 HOH A 10 510 10 HOH HOH . G 5 HOH A 11 511 11 HOH HOH . G 5 HOH A 12 512 12 HOH HOH . G 5 HOH A 13 513 14 HOH HOH . G 5 HOH A 14 514 15 HOH HOH . G 5 HOH A 15 515 16 HOH HOH . G 5 HOH A 16 516 17 HOH HOH . G 5 HOH A 17 517 18 HOH HOH . G 5 HOH A 18 518 19 HOH HOH . G 5 HOH A 19 519 20 HOH HOH . G 5 HOH A 20 520 21 HOH HOH . G 5 HOH A 21 521 22 HOH HOH . G 5 HOH A 22 522 23 HOH HOH . G 5 HOH A 23 523 24 HOH HOH . G 5 HOH A 24 524 25 HOH HOH . G 5 HOH A 25 525 26 HOH HOH . G 5 HOH A 26 526 27 HOH HOH . G 5 HOH A 27 527 28 HOH HOH . G 5 HOH A 28 528 29 HOH HOH . G 5 HOH A 29 529 30 HOH HOH . G 5 HOH A 30 530 31 HOH HOH . G 5 HOH A 31 531 32 HOH HOH . G 5 HOH A 32 532 33 HOH HOH . G 5 HOH A 33 533 34 HOH HOH . G 5 HOH A 34 534 35 HOH HOH . G 5 HOH A 35 535 36 HOH HOH . G 5 HOH A 36 536 37 HOH HOH . G 5 HOH A 37 537 38 HOH HOH . G 5 HOH A 38 538 39 HOH HOH . G 5 HOH A 39 539 40 HOH HOH . G 5 HOH A 40 540 41 HOH HOH . G 5 HOH A 41 541 42 HOH HOH . G 5 HOH A 42 542 43 HOH HOH . G 5 HOH A 43 543 44 HOH HOH . G 5 HOH A 44 544 45 HOH HOH . G 5 HOH A 45 545 46 HOH HOH . G 5 HOH A 46 546 47 HOH HOH . G 5 HOH A 47 547 49 HOH HOH . G 5 HOH A 48 548 50 HOH HOH . G 5 HOH A 49 549 51 HOH HOH . G 5 HOH A 50 550 52 HOH HOH . G 5 HOH A 51 551 53 HOH HOH . G 5 HOH A 52 552 54 HOH HOH . G 5 HOH A 53 553 55 HOH HOH . G 5 HOH A 54 554 56 HOH HOH . G 5 HOH A 55 555 57 HOH HOH . G 5 HOH A 56 556 58 HOH HOH . G 5 HOH A 57 557 59 HOH HOH . G 5 HOH A 58 558 60 HOH HOH . G 5 HOH A 59 559 61 HOH HOH . G 5 HOH A 60 560 62 HOH HOH . G 5 HOH A 61 561 63 HOH HOH . G 5 HOH A 62 562 64 HOH HOH . G 5 HOH A 63 563 65 HOH HOH . G 5 HOH A 64 564 66 HOH HOH . G 5 HOH A 65 565 68 HOH HOH . G 5 HOH A 66 566 69 HOH HOH . G 5 HOH A 67 567 70 HOH HOH . G 5 HOH A 68 568 72 HOH HOH . G 5 HOH A 69 569 73 HOH HOH . G 5 HOH A 70 570 74 HOH HOH . G 5 HOH A 71 571 75 HOH HOH . G 5 HOH A 72 572 76 HOH HOH . G 5 HOH A 73 573 77 HOH HOH . G 5 HOH A 74 574 78 HOH HOH . G 5 HOH A 75 575 79 HOH HOH . G 5 HOH A 76 576 80 HOH HOH . G 5 HOH A 77 577 81 HOH HOH . G 5 HOH A 78 578 82 HOH HOH . G 5 HOH A 79 579 83 HOH HOH . G 5 HOH A 80 580 84 HOH HOH . G 5 HOH A 81 581 85 HOH HOH . G 5 HOH A 82 582 86 HOH HOH . G 5 HOH A 83 583 87 HOH HOH . G 5 HOH A 84 584 88 HOH HOH . G 5 HOH A 85 585 89 HOH HOH . G 5 HOH A 86 586 90 HOH HOH . G 5 HOH A 87 587 91 HOH HOH . G 5 HOH A 88 588 92 HOH HOH . G 5 HOH A 89 589 93 HOH HOH . G 5 HOH A 90 590 94 HOH HOH . G 5 HOH A 91 591 95 HOH HOH . G 5 HOH A 92 592 96 HOH HOH . G 5 HOH A 93 593 97 HOH HOH . G 5 HOH A 94 594 98 HOH HOH . G 5 HOH A 95 595 99 HOH HOH . G 5 HOH A 96 596 100 HOH HOH . G 5 HOH A 97 597 101 HOH HOH . G 5 HOH A 98 598 102 HOH HOH . G 5 HOH A 99 599 103 HOH HOH . G 5 HOH A 100 600 104 HOH HOH . G 5 HOH A 101 601 105 HOH HOH . G 5 HOH A 102 602 106 HOH HOH . G 5 HOH A 103 603 107 HOH HOH . G 5 HOH A 104 604 108 HOH HOH . G 5 HOH A 105 605 109 HOH HOH . G 5 HOH A 106 606 110 HOH HOH . G 5 HOH A 107 607 111 HOH HOH . G 5 HOH A 108 608 112 HOH HOH . G 5 HOH A 109 609 113 HOH HOH . G 5 HOH A 110 610 114 HOH HOH . G 5 HOH A 111 611 115 HOH HOH . G 5 HOH A 112 612 116 HOH HOH . G 5 HOH A 113 613 117 HOH HOH . G 5 HOH A 114 614 118 HOH HOH . G 5 HOH A 115 615 119 HOH HOH . G 5 HOH A 116 616 120 HOH HOH . G 5 HOH A 117 617 121 HOH HOH . G 5 HOH A 118 618 122 HOH HOH . G 5 HOH A 119 619 123 HOH HOH . G 5 HOH A 120 620 124 HOH HOH . G 5 HOH A 121 621 125 HOH HOH . G 5 HOH A 122 622 126 HOH HOH . G 5 HOH A 123 623 127 HOH HOH . G 5 HOH A 124 624 128 HOH HOH . G 5 HOH A 125 625 130 HOH HOH . G 5 HOH A 126 626 131 HOH HOH . G 5 HOH A 127 627 132 HOH HOH . G 5 HOH A 128 628 133 HOH HOH . G 5 HOH A 129 629 134 HOH HOH . G 5 HOH A 130 630 135 HOH HOH . G 5 HOH A 131 631 136 HOH HOH . G 5 HOH A 132 632 137 HOH HOH . G 5 HOH A 133 633 138 HOH HOH . G 5 HOH A 134 634 139 HOH HOH . G 5 HOH A 135 635 140 HOH HOH . G 5 HOH A 136 636 141 HOH HOH . G 5 HOH A 137 637 142 HOH HOH . G 5 HOH A 138 638 143 HOH HOH . G 5 HOH A 139 639 144 HOH HOH . G 5 HOH A 140 640 145 HOH HOH . G 5 HOH A 141 641 146 HOH HOH . G 5 HOH A 142 642 147 HOH HOH . G 5 HOH A 143 643 148 HOH HOH . G 5 HOH A 144 644 149 HOH HOH . G 5 HOH A 145 645 150 HOH HOH . G 5 HOH A 146 646 151 HOH HOH . G 5 HOH A 147 647 152 HOH HOH . G 5 HOH A 148 648 153 HOH HOH . G 5 HOH A 149 649 154 HOH HOH . G 5 HOH A 150 650 155 HOH HOH . G 5 HOH A 151 651 156 HOH HOH . G 5 HOH A 152 652 157 HOH HOH . G 5 HOH A 153 653 158 HOH HOH . G 5 HOH A 154 654 159 HOH HOH . G 5 HOH A 155 655 160 HOH HOH . G 5 HOH A 156 656 161 HOH HOH . G 5 HOH A 157 657 162 HOH HOH . G 5 HOH A 158 658 163 HOH HOH . G 5 HOH A 159 659 164 HOH HOH . G 5 HOH A 160 660 165 HOH HOH . G 5 HOH A 161 661 166 HOH HOH . G 5 HOH A 162 662 167 HOH HOH . G 5 HOH A 163 663 168 HOH HOH . G 5 HOH A 164 664 169 HOH HOH . G 5 HOH A 165 665 170 HOH HOH . G 5 HOH A 166 666 171 HOH HOH . G 5 HOH A 167 667 172 HOH HOH . G 5 HOH A 168 668 173 HOH HOH . G 5 HOH A 169 669 174 HOH HOH . G 5 HOH A 170 670 175 HOH HOH . G 5 HOH A 171 671 176 HOH HOH . G 5 HOH A 172 672 177 HOH HOH . G 5 HOH A 173 673 178 HOH HOH . G 5 HOH A 174 674 179 HOH HOH . G 5 HOH A 175 675 180 HOH HOH . G 5 HOH A 176 676 181 HOH HOH . G 5 HOH A 177 677 182 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 O O17 ZOL . . . E 3 16.65 35.699 -6.656 1 38.96 ? O17 ZOL 404 A 1 HETATM 2 P P14 ZOL . . . E 3 15.289 35.726 -7.321 1 35.44 ? P14 ZOL 404 A 1 HETATM 3 O O16 ZOL . . . E 3 15.194 36.999 -8.205 1 33.2 ? O16 ZOL 404 A 1 HETATM 4 O O15 ZOL . . . E 3 14.262 35.708 -6.251 1 32.22 ? O15 ZOL 404 A 1 HETATM 5 C C8 ZOL . . . E 3 15.027 34.267 -8.37 1 36.03 ? C8 ZOL 404 A 1 HETATM 6 P P9 ZOL . . . E 3 16.354 34.188 -9.678 1 35.94 ? P9 ZOL 404 A 1 HETATM 7 O O10 ZOL . . . E 3 16.091 32.977 -10.645 1 32.87 ? O10 ZOL 404 A 1 HETATM 8 O O11 ZOL . . . E 3 16.198 35.508 -10.437 1 40.64 ? O11 ZOL 404 A 1 HETATM 9 O O12 ZOL . . . E 3 17.739 34.144 -9.131 1 36.88 ? O12 ZOL 404 A 1 HETATM 10 O O13 ZOL . . . E 3 13.823 34.45 -9.118 1 35.91 ? O13 ZOL 404 A 1 HETATM 11 C C7 ZOL . . . E 3 14.964 33.007 -7.507 1 35.82 ? C7 ZOL 404 A 1 HETATM 12 N N15 ZOL . . . E 3 14.716 31.74 -8.175 1 37.89 ? N15 ZOL 404 A 1 HETATM 13 C C16 ZOL . . . E 3 13.687 31.45 -8.948 1 34.23 ? C16 ZOL 404 A 1 HETATM 14 N N17 ZOL . . . E 3 13.858 30.22 -9.433 1 35.84 ? N17 ZOL 404 A 1 HETATM 15 C C18 ZOL . . . E 3 14.998 29.699 -8.947 1 38.07 ? C18 ZOL 404 A 1 HETATM 16 C C19 ZOL . . . E 3 15.56 30.668 -8.154 1 38.88 ? C19 ZOL 404 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 232 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 16 #