data_7KJ8 # _model_server_result.job_id k_HGxIwXgchuHTY5ApKhRw _model_server_result.datetime_utc '2024-11-25 07:57:45' _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 7kj8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 7KJ8 # _exptl.entry_id 7KJ8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 235.069 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description PAMIDRONATE _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 96.69 _cell.angle_gamma 90 _cell.entry_id 7KJ8 _cell.length_a 52.54 _cell.length_b 46.89 _cell.length_c 75.47 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KJ8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 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 4 _struct_asym.id F _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 120 A ASP 99 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc2 A OD1 ASP 120 A ASP 99 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc3 A OD1 ASN 261 A ASN 240 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc4 A OG SER 265 A SER 244 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc5 A OE2 GLU 269 A GLU 248 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc6 B MG MG . A MG 401 1_555 F O5 210 . A 210 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc7 B MG MG . A MG 401 1_555 F O9 210 . A 210 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc8 B MG MG . A MG 401 1_555 G O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc9 C MG MG . A MG 402 1_555 F O2 210 . A 210 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc10 C MG MG . A MG 402 1_555 F O10 210 . A 210 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc11 C MG MG . A MG 402 1_555 G O HOH . A HOH 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc12 C MG MG . A MG 402 1_555 G O HOH . A HOH 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc13 C MG MG . A MG 402 1_555 G O HOH . A HOH 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc14 D MG MG . A MG 403 1_555 F O10 210 . A 210 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc15 D MG MG . A MG 403 1_555 G O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc16 D MG MG . A MG 403 1_555 G O HOH . A HOH 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc17 D MG MG . A MG 403 1_555 G O HOH . A HOH 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc18 D MG MG . A MG 403 1_555 G O HOH . A HOH 576 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? # _chem_comp.formula 'C3 H11 N O7 P2' _chem_comp.formula_weight 235.069 _chem_comp.id 210 _chem_comp.mon_nstd_flag . _chem_comp.name PAMIDRONATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(3-AMINO-1-HYDROXY-1-PHOSPHONO-PROPYL)PHOSPHONIC 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 P1 O2 210 sing 1 n n P1 O3 210 sing 2 n n P1 O5 210 doub 3 n n P1 C7 210 sing 4 n n O2 HO2 210 sing 5 n n O3 HO3 210 sing 6 n n C7 P8 210 sing 7 n n C7 O14 210 sing 8 n n C7 C16 210 sing 9 n n P8 O9 210 doub 10 n n P8 O10 210 sing 11 n n P8 O12 210 sing 12 n n O10 HO10 210 sing 13 n n O12 HO12 210 sing 14 n n O14 HO14 210 sing 15 n n C16 C19 210 sing 16 n n C16 H161 210 sing 17 n n C16 H162 210 sing 18 n n C19 N22 210 sing 19 n n C19 H191 210 sing 20 n n C19 H192 210 sing 21 n n N22 H221 210 sing 22 n n N22 H222 210 sing 23 n n # _atom_sites.entry_id 7KJ8 _atom_sites.fract_transf_matrix[1][1] 0.019033 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002233 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021327 _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] 0.013341 _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 1 MG MG . C 2 MG A 1 402 2 MG MG . D 2 MG A 1 403 3 MG MG . E 3 SO4 A 1 404 1 SO4 SO4 . F 4 210 A 1 405 1 210 LIG . G 5 HOH A 1 501 6 HOH HOH . G 5 HOH A 2 502 59 HOH HOH . G 5 HOH A 3 503 192 HOH HOH . G 5 HOH A 4 504 82 HOH HOH . G 5 HOH A 5 505 84 HOH HOH . G 5 HOH A 6 506 39 HOH HOH . G 5 HOH A 7 507 106 HOH HOH . G 5 HOH A 8 508 20 HOH HOH . G 5 HOH A 9 509 22 HOH HOH . G 5 HOH A 10 510 45 HOH HOH . G 5 HOH A 11 511 173 HOH HOH . G 5 HOH A 12 512 125 HOH HOH . G 5 HOH A 13 513 11 HOH HOH . G 5 HOH A 14 514 43 HOH HOH . G 5 HOH A 15 515 95 HOH HOH . G 5 HOH A 16 516 32 HOH HOH . G 5 HOH A 17 517 16 HOH HOH . G 5 HOH A 18 518 27 HOH HOH . G 5 HOH A 19 519 107 HOH HOH . G 5 HOH A 20 520 13 HOH HOH . G 5 HOH A 21 521 5 HOH HOH . G 5 HOH A 22 522 75 HOH HOH . G 5 HOH A 23 523 80 HOH HOH . G 5 HOH A 24 524 123 HOH HOH . G 5 HOH A 25 525 42 HOH HOH . G 5 HOH A 26 526 71 HOH HOH . G 5 HOH A 27 527 12 HOH HOH . G 5 HOH A 28 528 10 HOH HOH . G 5 HOH A 29 529 166 HOH HOH . G 5 HOH A 30 530 34 HOH HOH . G 5 HOH A 31 531 35 HOH HOH . G 5 HOH A 32 532 99 HOH HOH . G 5 HOH A 33 533 66 HOH HOH . G 5 HOH A 34 534 131 HOH HOH . G 5 HOH A 35 535 18 HOH HOH . G 5 HOH A 36 536 23 HOH HOH . G 5 HOH A 37 537 88 HOH HOH . G 5 HOH A 38 538 26 HOH HOH . G 5 HOH A 39 539 60 HOH HOH . G 5 HOH A 40 540 58 HOH HOH . G 5 HOH A 41 541 90 HOH HOH . G 5 HOH A 42 542 97 HOH HOH . G 5 HOH A 43 543 115 HOH HOH . G 5 HOH A 44 544 93 HOH HOH . G 5 HOH A 45 545 167 HOH HOH . G 5 HOH A 46 546 47 HOH HOH . G 5 HOH A 47 547 3 HOH HOH . G 5 HOH A 48 548 14 HOH HOH . G 5 HOH A 49 549 132 HOH HOH . G 5 HOH A 50 550 21 HOH HOH . G 5 HOH A 51 551 79 HOH HOH . G 5 HOH A 52 552 31 HOH HOH . G 5 HOH A 53 553 67 HOH HOH . G 5 HOH A 54 554 144 HOH HOH . G 5 HOH A 55 555 161 HOH HOH . G 5 HOH A 56 556 4 HOH HOH . G 5 HOH A 57 557 2 HOH HOH . G 5 HOH A 58 558 152 HOH HOH . G 5 HOH A 59 559 153 HOH HOH . G 5 HOH A 60 560 70 HOH HOH . G 5 HOH A 61 561 77 HOH HOH . G 5 HOH A 62 562 168 HOH HOH . G 5 HOH A 63 563 56 HOH HOH . G 5 HOH A 64 564 183 HOH HOH . G 5 HOH A 65 565 1 HOH HOH . G 5 HOH A 66 566 65 HOH HOH . G 5 HOH A 67 567 25 HOH HOH . G 5 HOH A 68 568 50 HOH HOH . G 5 HOH A 69 569 53 HOH HOH . G 5 HOH A 70 570 73 HOH HOH . G 5 HOH A 71 571 33 HOH HOH . G 5 HOH A 72 572 92 HOH HOH . G 5 HOH A 73 573 112 HOH HOH . G 5 HOH A 74 574 105 HOH HOH . G 5 HOH A 75 575 8 HOH HOH . G 5 HOH A 76 576 17 HOH HOH . G 5 HOH A 77 577 7 HOH HOH . G 5 HOH A 78 578 83 HOH HOH . G 5 HOH A 79 579 100 HOH HOH . G 5 HOH A 80 580 108 HOH HOH . G 5 HOH A 81 581 63 HOH HOH . G 5 HOH A 82 582 36 HOH HOH . G 5 HOH A 83 583 49 HOH HOH . G 5 HOH A 84 584 91 HOH HOH . G 5 HOH A 85 585 170 HOH HOH . G 5 HOH A 86 586 129 HOH HOH . G 5 HOH A 87 587 117 HOH HOH . G 5 HOH A 88 588 40 HOH HOH . G 5 HOH A 89 589 142 HOH HOH . G 5 HOH A 90 590 104 HOH HOH . G 5 HOH A 91 591 19 HOH HOH . G 5 HOH A 92 592 146 HOH HOH . G 5 HOH A 93 593 78 HOH HOH . G 5 HOH A 94 594 110 HOH HOH . G 5 HOH A 95 595 74 HOH HOH . G 5 HOH A 96 596 113 HOH HOH . G 5 HOH A 97 597 156 HOH HOH . G 5 HOH A 98 598 29 HOH HOH . G 5 HOH A 99 599 28 HOH HOH . G 5 HOH A 100 600 64 HOH HOH . G 5 HOH A 101 601 226 HOH HOH . G 5 HOH A 102 602 164 HOH HOH . G 5 HOH A 103 603 126 HOH HOH . G 5 HOH A 104 604 103 HOH HOH . G 5 HOH A 105 605 109 HOH HOH . G 5 HOH A 106 606 162 HOH HOH . G 5 HOH A 107 607 62 HOH HOH . G 5 HOH A 108 608 37 HOH HOH . G 5 HOH A 109 609 121 HOH HOH . G 5 HOH A 110 610 38 HOH HOH . G 5 HOH A 111 611 159 HOH HOH . G 5 HOH A 112 612 69 HOH HOH . G 5 HOH A 113 613 151 HOH HOH . G 5 HOH A 114 614 9 HOH HOH . G 5 HOH A 115 615 145 HOH HOH . G 5 HOH A 116 616 15 HOH HOH . G 5 HOH A 117 617 169 HOH HOH . G 5 HOH A 118 618 101 HOH HOH . G 5 HOH A 119 619 68 HOH HOH . G 5 HOH A 120 620 134 HOH HOH . G 5 HOH A 121 621 76 HOH HOH . G 5 HOH A 122 622 94 HOH HOH . G 5 HOH A 123 623 96 HOH HOH . G 5 HOH A 124 624 111 HOH HOH . G 5 HOH A 125 625 41 HOH HOH . G 5 HOH A 126 626 171 HOH HOH . G 5 HOH A 127 627 30 HOH HOH . G 5 HOH A 128 628 147 HOH HOH . G 5 HOH A 129 629 51 HOH HOH . G 5 HOH A 130 630 139 HOH HOH . G 5 HOH A 131 631 44 HOH HOH . G 5 HOH A 132 632 72 HOH HOH . G 5 HOH A 133 633 85 HOH HOH . G 5 HOH A 134 634 150 HOH HOH . G 5 HOH A 135 635 120 HOH HOH . G 5 HOH A 136 636 232 HOH HOH . G 5 HOH A 137 637 52 HOH HOH . G 5 HOH A 138 638 46 HOH HOH . G 5 HOH A 139 639 165 HOH HOH . G 5 HOH A 140 640 225 HOH HOH . G 5 HOH A 141 641 24 HOH HOH . G 5 HOH A 142 642 141 HOH HOH . G 5 HOH A 143 643 138 HOH HOH . G 5 HOH A 144 644 87 HOH HOH . G 5 HOH A 145 645 135 HOH HOH . G 5 HOH A 146 646 195 HOH HOH . G 5 HOH A 147 647 48 HOH HOH . G 5 HOH A 148 648 116 HOH HOH . G 5 HOH A 149 649 158 HOH HOH . G 5 HOH A 150 650 230 HOH HOH . G 5 HOH A 151 651 149 HOH HOH . G 5 HOH A 152 652 233 HOH HOH . G 5 HOH A 153 653 130 HOH HOH . G 5 HOH A 154 654 172 HOH HOH . G 5 HOH A 155 655 124 HOH HOH . G 5 HOH A 156 656 61 HOH HOH . G 5 HOH A 157 657 231 HOH HOH . G 5 HOH A 158 658 118 HOH HOH . G 5 HOH A 159 659 140 HOH HOH . G 5 HOH A 160 660 102 HOH HOH . G 5 HOH A 161 661 136 HOH HOH . G 5 HOH A 162 662 176 HOH HOH . G 5 HOH A 163 663 175 HOH HOH . G 5 HOH A 164 664 114 HOH HOH . G 5 HOH A 165 665 193 HOH HOH . G 5 HOH A 166 666 188 HOH HOH . G 5 HOH A 167 667 54 HOH HOH . G 5 HOH A 168 668 81 HOH HOH . G 5 HOH A 169 669 148 HOH HOH . G 5 HOH A 170 670 229 HOH HOH . G 5 HOH A 171 671 143 HOH HOH . G 5 HOH A 172 672 127 HOH HOH . G 5 HOH A 173 673 122 HOH HOH . G 5 HOH A 174 674 57 HOH HOH . G 5 HOH A 175 675 133 HOH HOH . G 5 HOH A 176 676 160 HOH HOH . G 5 HOH A 177 677 86 HOH HOH . G 5 HOH A 178 678 55 HOH HOH . G 5 HOH A 179 679 179 HOH HOH . G 5 HOH A 180 680 89 HOH HOH . G 5 HOH A 181 681 182 HOH HOH . G 5 HOH A 182 682 137 HOH HOH . G 5 HOH A 183 683 214 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 P P1 210 . . . F 4 10.764 -0.661 19.657 1 22.63 ? P1 210 405 A 1 HETATM 2 O O2 210 . . . F 4 11.403 -0.756 21.017 1 23.6 -1 O2 210 405 A 1 HETATM 3 O O3 210 . . . F 4 10.884 0.766 19.118 1 18.35 -1 O3 210 405 A 1 HETATM 4 O O5 210 . . . F 4 11.436 -1.609 18.696 1 17.14 ? O5 210 405 A 1 HETATM 5 C C7 210 . . . F 4 8.971 -1.119 19.822 1 18.65 ? C7 210 405 A 1 HETATM 6 P P8 210 . . . F 4 8.812 -2.812 20.543 1 17.89 ? P8 210 405 A 1 HETATM 7 O O9 210 . . . F 4 9.661 -3.744 19.683 1 16.66 -1 O9 210 405 A 1 HETATM 8 O O10 210 . . . F 4 9.272 -2.745 21.98 1 19.35 ? O10 210 405 A 1 HETATM 9 O O12 210 . . . F 4 7.339 -3.129 20.461 1 18.38 -1 O12 210 405 A 1 HETATM 10 O O14 210 . . . F 4 8.357 -1.195 18.566 1 22.88 ? O14 210 405 A 1 HETATM 11 C C16 210 . . . F 4 8.241 -0.171 20.766 1 18.55 ? C16 210 405 A 1 HETATM 12 C C19 210 . . . F 4 6.903 0.249 20.172 1 27.01 ? C19 210 405 A 1 HETATM 13 N N22 210 . . . F 4 5.942 -0.823 20.237 1 22.93 ? N22 210 405 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 13 #