data_4KPD # _model_server_result.job_id i_tYpi5j4cZUdN3VTFVORw _model_server_result.datetime_utc '2024-11-25 05:17:58' _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 4kpd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 4KPD # _exptl.entry_id 4KPD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 283.112 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC 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 4KPD _cell.length_a 111.73 _cell.length_b 111.73 _cell.length_c 66.99 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KPD _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' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -33.495 # _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 125 A ASP 103 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc2 A OD1 ASP 125 A ASP 103 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc3 A OD2 ASP 129 A ASP 107 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc4 A OD2 ASP 129 A ASP 107 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc5 A OD2 ASP 265 A ASP 243 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc6 B MG MG . A MG 401 1_555 F O15 RIS . A RIS 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc7 B MG MG . A MG 401 1_555 F O12 RIS . A RIS 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc8 B MG MG . A MG 401 1_555 G O HOH . A HOH 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? metalc ? metalc9 B MG MG . A MG 401 1_555 G O HOH . A HOH 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc10 B MG MG . A MG 401 1_555 G O HOH . A HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc11 C MG MG . A MG 402 1_555 F O16 RIS . A RIS 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc12 C MG MG . A MG 402 1_555 F O11 RIS . A RIS 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc13 C MG MG . A MG 402 1_555 G O HOH . A HOH 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc14 C MG MG . A MG 402 1_555 G O HOH . A HOH 578 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc15 C MG MG . A MG 402 1_555 G O HOH . A HOH 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc16 D MG MG . A MG 403 1_555 F O15 RIS . A RIS 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc17 D MG MG . A MG 403 1_555 G O HOH . A HOH 573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc18 D MG MG . A MG 403 1_555 G O HOH . A HOH 574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc19 D MG MG . A MG 403 1_555 G O HOH . A HOH 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? # _chem_comp.formula 'C7 H11 N O7 P2' _chem_comp.formula_weight 283.112 _chem_comp.id RIS _chem_comp.mon_nstd_flag . _chem_comp.name '1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Risedronate # 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 O12 P9 RIS sing 302 n n O12 H12 RIS sing 303 n n P9 O11 RIS doub 304 n n P9 O10 RIS sing 305 n n P9 C8 RIS sing 306 n n C8 O13 RIS sing 307 n n C8 P14 RIS sing 308 n n C8 C7 RIS sing 309 n n O13 H13 RIS sing 310 n n P14 O16 RIS sing 311 n n P14 O15 RIS sing 312 n n P14 O17 RIS doub 313 n n O16 H16 RIS sing 314 n n O15 H15 RIS sing 315 n n C7 C2 RIS sing 316 n n C7 HC71 RIS sing 317 n n C7 HC72 RIS sing 318 n n C2 C1 RIS doub 319 n y C2 C3 RIS sing 320 n y C1 C6 RIS sing 321 n y C1 HC1 RIS sing 322 n n C6 C5 RIS doub 323 n y C6 HC6 RIS sing 324 n n C5 N4 RIS sing 325 n y C5 HC5 RIS sing 326 n n N4 C3 RIS doub 327 n y C3 HC3 RIS sing 328 n n HO1 O10 RIS sing 329 n n # _atom_sites.entry_id 4KPD _atom_sites.fract_transf_matrix[1][1] 0.00895 _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] 0.00895 _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] 0.014928 _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 IPE A 1 404 900 IPE IPE . F 4 RIS A 1 405 901 RIS RIS . G 5 HOH A 1 501 10 HOH HOH . G 5 HOH A 2 502 11 HOH HOH . G 5 HOH A 3 503 13 HOH HOH . G 5 HOH A 4 504 14 HOH HOH . G 5 HOH A 5 505 15 HOH HOH . G 5 HOH A 6 506 16 HOH HOH . G 5 HOH A 7 507 17 HOH HOH . G 5 HOH A 8 508 19 HOH HOH . G 5 HOH A 9 509 20 HOH HOH . G 5 HOH A 10 510 24 HOH HOH . G 5 HOH A 11 511 25 HOH HOH . G 5 HOH A 12 512 26 HOH HOH . G 5 HOH A 13 513 27 HOH HOH . G 5 HOH A 14 514 28 HOH HOH . G 5 HOH A 15 515 29 HOH HOH . G 5 HOH A 16 516 30 HOH HOH . G 5 HOH A 17 517 31 HOH HOH . G 5 HOH A 18 518 32 HOH HOH . G 5 HOH A 19 519 36 HOH HOH . G 5 HOH A 20 520 37 HOH HOH . G 5 HOH A 21 521 39 HOH HOH . G 5 HOH A 22 522 40 HOH HOH . G 5 HOH A 23 523 41 HOH HOH . G 5 HOH A 24 524 43 HOH HOH . G 5 HOH A 25 525 45 HOH HOH . G 5 HOH A 26 526 47 HOH HOH . G 5 HOH A 27 527 49 HOH HOH . G 5 HOH A 28 528 50 HOH HOH . G 5 HOH A 29 529 51 HOH HOH . G 5 HOH A 30 530 52 HOH HOH . G 5 HOH A 31 531 53 HOH HOH . G 5 HOH A 32 532 55 HOH HOH . G 5 HOH A 33 533 57 HOH HOH . G 5 HOH A 34 534 58 HOH HOH . G 5 HOH A 35 535 59 HOH HOH . G 5 HOH A 36 536 60 HOH HOH . G 5 HOH A 37 537 61 HOH HOH . G 5 HOH A 38 538 62 HOH HOH . G 5 HOH A 39 539 66 HOH HOH . G 5 HOH A 40 540 72 HOH HOH . G 5 HOH A 41 541 73 HOH HOH . G 5 HOH A 42 542 75 HOH HOH . G 5 HOH A 43 543 77 HOH HOH . G 5 HOH A 44 544 79 HOH HOH . G 5 HOH A 45 545 80 HOH HOH . G 5 HOH A 46 546 81 HOH HOH . G 5 HOH A 47 547 82 HOH HOH . G 5 HOH A 48 548 83 HOH HOH . G 5 HOH A 49 549 86 HOH HOH . G 5 HOH A 50 550 87 HOH HOH . G 5 HOH A 51 551 88 HOH HOH . G 5 HOH A 52 552 91 HOH HOH . G 5 HOH A 53 553 93 HOH HOH . G 5 HOH A 54 554 99 HOH HOH . G 5 HOH A 55 555 100 HOH HOH . G 5 HOH A 56 556 101 HOH HOH . G 5 HOH A 57 557 104 HOH HOH . G 5 HOH A 58 558 106 HOH HOH . G 5 HOH A 59 559 107 HOH HOH . G 5 HOH A 60 560 108 HOH HOH . G 5 HOH A 61 561 112 HOH HOH . G 5 HOH A 62 562 114 HOH HOH . G 5 HOH A 63 563 115 HOH HOH . G 5 HOH A 64 564 116 HOH HOH . G 5 HOH A 65 565 117 HOH HOH . G 5 HOH A 66 566 119 HOH HOH . G 5 HOH A 67 567 122 HOH HOH . G 5 HOH A 68 568 123 HOH HOH . G 5 HOH A 69 569 124 HOH HOH . G 5 HOH A 70 570 127 HOH HOH . G 5 HOH A 71 571 129 HOH HOH . G 5 HOH A 72 572 130 HOH HOH . G 5 HOH A 73 573 132 HOH HOH . G 5 HOH A 74 574 133 HOH HOH . G 5 HOH A 75 575 134 HOH HOH . G 5 HOH A 76 576 135 HOH HOH . G 5 HOH A 77 577 136 HOH HOH . G 5 HOH A 78 578 137 HOH HOH . G 5 HOH A 79 579 138 HOH HOH . G 5 HOH A 80 580 139 HOH HOH . G 5 HOH A 81 581 140 HOH HOH . G 5 HOH A 82 582 141 HOH HOH . G 5 HOH A 83 583 142 HOH HOH . G 5 HOH A 84 584 143 HOH HOH . G 5 HOH A 85 585 144 HOH HOH . G 5 HOH A 86 586 145 HOH HOH . G 5 HOH A 87 587 146 HOH HOH . G 5 HOH A 88 588 147 HOH HOH . G 5 HOH A 89 589 148 HOH HOH . G 5 HOH A 90 590 149 HOH HOH . G 5 HOH A 91 591 150 HOH HOH . G 5 HOH A 92 592 151 HOH HOH . G 5 HOH A 93 593 152 HOH HOH . G 5 HOH A 94 594 154 HOH HOH . G 5 HOH A 95 595 155 HOH HOH . G 5 HOH A 96 596 156 HOH HOH . G 5 HOH A 97 597 157 HOH HOH . G 5 HOH A 98 598 158 HOH HOH . G 5 HOH A 99 599 159 HOH HOH . G 5 HOH A 100 600 161 HOH HOH . G 5 HOH A 101 601 163 HOH HOH . G 5 HOH A 102 602 166 HOH HOH . G 5 HOH A 103 603 168 HOH HOH . G 5 HOH A 104 604 171 HOH HOH . G 5 HOH A 105 605 173 HOH HOH . G 5 HOH A 106 606 174 HOH HOH . G 5 HOH A 107 607 175 HOH HOH . G 5 HOH A 108 608 176 HOH HOH . G 5 HOH A 109 609 178 HOH HOH . G 5 HOH A 110 610 179 HOH HOH . G 5 HOH A 111 611 181 HOH HOH . G 5 HOH A 112 612 182 HOH HOH . G 5 HOH A 113 613 183 HOH HOH . G 5 HOH A 114 614 184 HOH HOH . G 5 HOH A 115 615 185 HOH HOH . G 5 HOH A 116 616 186 HOH HOH . G 5 HOH A 117 617 188 HOH HOH . G 5 HOH A 118 618 189 HOH HOH . G 5 HOH A 119 619 190 HOH HOH . G 5 HOH A 120 620 191 HOH HOH . G 5 HOH A 121 621 192 HOH HOH . G 5 HOH A 122 622 193 HOH HOH . G 5 HOH A 123 623 194 HOH HOH . G 5 HOH A 124 624 195 HOH HOH . G 5 HOH A 125 625 196 HOH HOH . G 5 HOH A 126 626 197 HOH HOH . G 5 HOH A 127 627 198 HOH HOH . G 5 HOH A 128 628 199 HOH HOH . G 5 HOH A 129 629 200 HOH HOH . G 5 HOH A 130 630 201 HOH HOH . G 5 HOH A 131 631 202 HOH HOH . G 5 HOH A 132 632 203 HOH HOH . G 5 HOH A 133 633 204 HOH HOH . G 5 HOH A 134 634 205 HOH HOH . G 5 HOH A 135 635 206 HOH HOH . G 5 HOH A 136 636 207 HOH HOH . G 5 HOH A 137 637 208 HOH HOH . G 5 HOH A 138 638 209 HOH HOH . G 5 HOH A 139 639 210 HOH HOH . G 5 HOH A 140 640 211 HOH HOH . G 5 HOH A 141 641 212 HOH HOH . G 5 HOH A 142 642 213 HOH HOH . G 5 HOH A 143 643 214 HOH HOH . G 5 HOH A 144 644 215 HOH HOH . G 5 HOH A 145 645 216 HOH HOH . G 5 HOH A 146 646 217 HOH HOH . G 5 HOH A 147 647 218 HOH HOH . G 5 HOH A 148 648 219 HOH HOH . G 5 HOH A 149 649 220 HOH HOH . G 5 HOH A 150 650 221 HOH HOH . G 5 HOH A 151 651 222 HOH HOH . G 5 HOH A 152 652 223 HOH HOH . G 5 HOH A 153 653 224 HOH HOH . G 5 HOH A 154 654 225 HOH HOH . G 5 HOH A 155 655 226 HOH HOH . G 5 HOH A 156 656 227 HOH HOH . G 5 HOH A 157 657 228 HOH HOH . G 5 HOH A 158 658 229 HOH HOH . G 5 HOH A 159 659 230 HOH HOH . G 5 HOH A 160 660 231 HOH HOH . G 5 HOH A 161 661 232 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 O12 RIS . . . F 4 16.779 -35.67 -9.995 1 44.92 ? O12 RIS 405 A 1 HETATM 2 P P9 RIS . . . F 4 15.29 -35.669 -9.507 1 42.98 ? P9 RIS 405 A 1 HETATM 3 O O11 RIS . . . F 4 15.061 -36.865 -8.543 1 39.89 ? O11 RIS 405 A 1 HETATM 4 O O10 RIS . . . F 4 14.463 -35.829 -10.747 1 33.17 ? O10 RIS 405 A 1 HETATM 5 C C8 RIS . . . F 4 14.893 -34.144 -8.634 1 43.03 ? C8 RIS 405 A 1 HETATM 6 O O13 RIS . . . F 4 13.639 -34.311 -8.068 1 41.65 ? O13 RIS 405 A 1 HETATM 7 P P14 RIS . . . F 4 16.156 -34.113 -7.33 1 39.7 ? P14 RIS 405 A 1 HETATM 8 O O16 RIS . . . F 4 15.978 -35.436 -6.496 1 42.19 ? O16 RIS 405 A 1 HETATM 9 O O15 RIS . . . F 4 17.609 -34.072 -7.931 1 39.21 ? O15 RIS 405 A 1 HETATM 10 O O17 RIS . . . F 4 16.024 -32.961 -6.398 1 33.46 ? O17 RIS 405 A 1 HETATM 11 C C7 RIS . . . F 4 14.998 -32.978 -9.574 1 39.38 ? C7 RIS 405 A 1 HETATM 12 C C2 RIS . . . F 4 14.757 -31.569 -9.121 1 39.9 ? C2 RIS 405 A 1 HETATM 13 C C1 RIS . . . F 4 15.375 -30.542 -9.86 1 37.51 ? C1 RIS 405 A 1 HETATM 14 C C6 RIS . . . F 4 15.203 -29.225 -9.437 1 35.82 ? C6 RIS 405 A 1 HETATM 15 C C5 RIS . . . F 4 14.395 -28.966 -8.329 1 39.16 ? C5 RIS 405 A 1 HETATM 16 N N4 RIS . . . F 4 13.787 -29.964 -7.664 1 39.76 ? N4 RIS 405 A 1 HETATM 17 C C3 RIS . . . F 4 13.966 -31.249 -8.007 1 38.84 ? C3 RIS 405 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 17 #