data_4NKF # _model_server_result.job_id Hkow0DFABw7EKWSriw2L5A _model_server_result.datetime_utc '2024-12-01 09:03:25' _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 4nkf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":404}' # _entry.id 4NKF # _exptl.entry_id 4NKF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 235.069 _entity.id 3 _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 90 _cell.angle_gamma 90 _cell.entry_id 4NKF _cell.length_a 111.45 _cell.length_b 111.45 _cell.length_c 67.53 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NKF _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,H _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc2 A OD1 ASP 125 A ASP 103 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? metalc ? metalc3 A OD2 ASP 129 A ASP 107 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc4 A OD2 ASP 129 A ASP 107 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc5 A OD2 ASP 265 A ASP 243 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc6 B MG MG . A MG 401 1_555 E O2 210 . A 210 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc7 B MG MG . A MG 401 1_555 E O9 210 . A 210 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc8 B MG MG . A MG 401 1_555 H O HOH . A HOH 598 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? metalc ? metalc9 B MG MG . A MG 401 1_555 H O HOH . A HOH 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc10 C MG MG . A MG 402 1_555 E O3 210 . A 210 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc11 C MG MG . A MG 402 1_555 E O10 210 . A 210 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc12 C MG MG . A MG 402 1_555 H O HOH . A HOH 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc13 C MG MG . A MG 402 1_555 H O HOH . A HOH 592 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc14 C MG MG . A MG 402 1_555 H O HOH . A HOH 593 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc15 D MG MG . A MG 403 1_555 E O9 210 . A 210 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc16 D MG MG . A MG 403 1_555 H O HOH . A HOH 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc17 D MG MG . A MG 403 1_555 H O HOH . A HOH 596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc18 D MG MG . A MG 403 1_555 H O HOH . A HOH 597 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? # _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 4NKF _atom_sites.fract_transf_matrix[1][1] 0.008973 _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] 0.008973 _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] 0.014808 _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 3 210 A 1 404 901 210 210 . F 4 EDO A 1 405 1 EDO EDO . G 5 PEG A 1 406 2 PEG PEG . H 6 HOH A 1 501 3 HOH HOH . H 6 HOH A 2 502 4 HOH HOH . H 6 HOH A 3 503 5 HOH HOH . H 6 HOH A 4 504 6 HOH HOH . H 6 HOH A 5 505 8 HOH HOH . H 6 HOH A 6 506 9 HOH HOH . H 6 HOH A 7 507 10 HOH HOH . H 6 HOH A 8 508 11 HOH HOH . H 6 HOH A 9 509 12 HOH HOH . H 6 HOH A 10 510 13 HOH HOH . H 6 HOH A 11 511 14 HOH HOH . H 6 HOH A 12 512 16 HOH HOH . H 6 HOH A 13 513 17 HOH HOH . H 6 HOH A 14 514 18 HOH HOH . H 6 HOH A 15 515 19 HOH HOH . H 6 HOH A 16 516 20 HOH HOH . H 6 HOH A 17 517 22 HOH HOH . H 6 HOH A 18 518 23 HOH HOH . H 6 HOH A 19 519 24 HOH HOH . H 6 HOH A 20 520 25 HOH HOH . H 6 HOH A 21 521 26 HOH HOH . H 6 HOH A 22 522 27 HOH HOH . H 6 HOH A 23 523 29 HOH HOH . H 6 HOH A 24 524 30 HOH HOH . H 6 HOH A 25 525 31 HOH HOH . H 6 HOH A 26 526 32 HOH HOH . H 6 HOH A 27 527 33 HOH HOH . H 6 HOH A 28 528 35 HOH HOH . H 6 HOH A 29 529 36 HOH HOH . H 6 HOH A 30 530 38 HOH HOH . H 6 HOH A 31 531 39 HOH HOH . H 6 HOH A 32 532 40 HOH HOH . H 6 HOH A 33 533 41 HOH HOH . H 6 HOH A 34 534 42 HOH HOH . H 6 HOH A 35 535 43 HOH HOH . H 6 HOH A 36 536 44 HOH HOH . H 6 HOH A 37 537 46 HOH HOH . H 6 HOH A 38 538 49 HOH HOH . H 6 HOH A 39 539 50 HOH HOH . H 6 HOH A 40 540 51 HOH HOH . H 6 HOH A 41 541 52 HOH HOH . H 6 HOH A 42 542 53 HOH HOH . H 6 HOH A 43 543 55 HOH HOH . H 6 HOH A 44 544 56 HOH HOH . H 6 HOH A 45 545 58 HOH HOH . H 6 HOH A 46 546 63 HOH HOH . H 6 HOH A 47 547 64 HOH HOH . H 6 HOH A 48 548 65 HOH HOH . H 6 HOH A 49 549 66 HOH HOH . H 6 HOH A 50 550 68 HOH HOH . H 6 HOH A 51 551 69 HOH HOH . H 6 HOH A 52 552 71 HOH HOH . H 6 HOH A 53 553 72 HOH HOH . H 6 HOH A 54 554 74 HOH HOH . H 6 HOH A 55 555 75 HOH HOH . H 6 HOH A 56 556 76 HOH HOH . H 6 HOH A 57 557 78 HOH HOH . H 6 HOH A 58 558 80 HOH HOH . H 6 HOH A 59 559 81 HOH HOH . H 6 HOH A 60 560 82 HOH HOH . H 6 HOH A 61 561 85 HOH HOH . H 6 HOH A 62 562 89 HOH HOH . H 6 HOH A 63 563 91 HOH HOH . H 6 HOH A 64 564 93 HOH HOH . H 6 HOH A 65 565 94 HOH HOH . H 6 HOH A 66 566 96 HOH HOH . H 6 HOH A 67 567 97 HOH HOH . H 6 HOH A 68 568 99 HOH HOH . H 6 HOH A 69 569 100 HOH HOH . H 6 HOH A 70 570 101 HOH HOH . H 6 HOH A 71 571 102 HOH HOH . H 6 HOH A 72 572 104 HOH HOH . H 6 HOH A 73 573 106 HOH HOH . H 6 HOH A 74 574 107 HOH HOH . H 6 HOH A 75 575 109 HOH HOH . H 6 HOH A 76 576 114 HOH HOH . H 6 HOH A 77 577 115 HOH HOH . H 6 HOH A 78 578 121 HOH HOH . H 6 HOH A 79 579 124 HOH HOH . H 6 HOH A 80 580 126 HOH HOH . H 6 HOH A 81 581 127 HOH HOH . H 6 HOH A 82 582 128 HOH HOH . H 6 HOH A 83 583 134 HOH HOH . H 6 HOH A 84 584 142 HOH HOH . H 6 HOH A 85 585 144 HOH HOH . H 6 HOH A 86 586 148 HOH HOH . H 6 HOH A 87 587 151 HOH HOH . H 6 HOH A 88 588 155 HOH HOH . H 6 HOH A 89 589 157 HOH HOH . H 6 HOH A 90 590 158 HOH HOH . H 6 HOH A 91 591 159 HOH HOH . H 6 HOH A 92 592 160 HOH HOH . H 6 HOH A 93 593 161 HOH HOH . H 6 HOH A 94 594 162 HOH HOH . H 6 HOH A 95 595 163 HOH HOH . H 6 HOH A 96 596 164 HOH HOH . H 6 HOH A 97 597 165 HOH HOH . H 6 HOH A 98 598 166 HOH HOH . H 6 HOH A 99 599 167 HOH HOH . H 6 HOH A 100 600 168 HOH HOH . H 6 HOH A 101 601 169 HOH HOH . H 6 HOH A 102 602 172 HOH HOH . H 6 HOH A 103 603 173 HOH HOH . H 6 HOH A 104 604 174 HOH HOH . H 6 HOH A 105 605 175 HOH HOH . H 6 HOH A 106 606 176 HOH HOH . H 6 HOH A 107 607 178 HOH HOH . H 6 HOH A 108 608 180 HOH HOH . H 6 HOH A 109 609 185 HOH HOH . H 6 HOH A 110 610 186 HOH HOH . H 6 HOH A 111 611 188 HOH HOH . H 6 HOH A 112 612 189 HOH HOH . H 6 HOH A 113 613 190 HOH HOH . H 6 HOH A 114 614 191 HOH HOH . H 6 HOH A 115 615 194 HOH HOH . H 6 HOH A 116 616 197 HOH HOH . H 6 HOH A 117 617 198 HOH HOH . H 6 HOH A 118 618 199 HOH HOH . H 6 HOH A 119 619 200 HOH HOH . H 6 HOH A 120 620 203 HOH HOH . H 6 HOH A 121 621 206 HOH HOH . H 6 HOH A 122 622 207 HOH HOH . H 6 HOH A 123 623 208 HOH HOH . H 6 HOH A 124 624 211 HOH HOH . H 6 HOH A 125 625 212 HOH HOH . H 6 HOH A 126 626 214 HOH HOH . H 6 HOH A 127 627 215 HOH HOH . H 6 HOH A 128 628 216 HOH HOH . H 6 HOH A 129 629 218 HOH HOH . H 6 HOH A 130 630 220 HOH HOH . H 6 HOH A 131 631 221 HOH HOH . H 6 HOH A 132 632 223 HOH HOH . H 6 HOH A 133 633 224 HOH HOH . H 6 HOH A 134 634 225 HOH HOH . H 6 HOH A 135 635 226 HOH HOH . H 6 HOH A 136 636 227 HOH HOH . H 6 HOH A 137 637 229 HOH HOH . H 6 HOH A 138 638 230 HOH HOH . H 6 HOH A 139 639 231 HOH HOH . H 6 HOH A 140 640 232 HOH HOH . H 6 HOH A 141 641 233 HOH HOH . H 6 HOH A 142 642 234 HOH HOH . H 6 HOH A 143 643 235 HOH HOH . H 6 HOH A 144 644 236 HOH HOH . H 6 HOH A 145 645 237 HOH HOH . H 6 HOH A 146 646 238 HOH HOH . H 6 HOH A 147 647 239 HOH HOH . H 6 HOH A 148 648 240 HOH HOH . H 6 HOH A 149 649 241 HOH HOH . H 6 HOH A 150 650 242 HOH HOH . H 6 HOH A 151 651 243 HOH HOH . H 6 HOH A 152 652 244 HOH HOH . H 6 HOH A 153 653 245 HOH HOH . H 6 HOH A 154 654 246 HOH HOH . H 6 HOH A 155 655 247 HOH HOH . H 6 HOH A 156 656 248 HOH HOH . H 6 HOH A 157 657 249 HOH HOH . H 6 HOH A 158 658 250 HOH HOH . H 6 HOH A 159 659 251 HOH HOH . H 6 HOH A 160 660 252 HOH HOH . H 6 HOH A 161 661 253 HOH HOH . H 6 HOH A 162 662 254 HOH HOH . H 6 HOH A 163 663 255 HOH HOH . H 6 HOH A 164 664 256 HOH HOH . H 6 HOH A 165 665 257 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 . . . E 3 15.09 35.668 -7.496 1 33.38 ? P1 210 404 A 1 HETATM 2 O O2 210 . . . E 3 16.501 35.694 -6.811 1 34.27 ? O2 210 404 A 1 HETATM 3 O O3 210 . . . E 3 14.835 36.891 -8.394 1 32.18 ? O3 210 404 A 1 HETATM 4 O O5 210 . . . E 3 14.167 35.674 -6.313 1 28.3 ? O5 210 404 A 1 HETATM 5 C C7 210 . . . E 3 14.844 34.103 -8.41 1 37.01 ? C7 210 404 A 1 HETATM 6 P P8 210 . . . E 3 16.097 33.992 -9.697 1 35.21 ? P8 210 404 A 1 HETATM 7 O O9 210 . . . E 3 17.556 33.85 -9.116 1 30.21 ? O9 210 404 A 1 HETATM 8 O O10 210 . . . E 3 15.982 35.284 -10.564 1 36.08 ? O10 210 404 A 1 HETATM 9 O O12 210 . . . E 3 15.822 32.864 -10.641 1 34.36 ? O12 210 404 A 1 HETATM 10 O O14 210 . . . E 3 13.618 34.125 -9.055 1 37 ? O14 210 404 A 1 HETATM 11 C C16 210 . . . E 3 14.985 32.962 -7.457 1 37.93 ? C16 210 404 A 1 HETATM 12 C C19 210 . . . E 3 14.836 31.553 -7.943 1 41.73 ? C19 210 404 A 1 HETATM 13 N N22 210 . . . E 3 14.019 31.346 -9.114 1 40.67 ? N22 210 404 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 13 #