data_4P0W # _model_server_result.job_id '_EbP-BG8t3VJyLi62N-0OA' _model_server_result.datetime_utc '2025-02-02 13:55:04' _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 4p0w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 4P0W # _exptl.entry_id 4P0W _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 4P0W _cell.length_a 111.239 _cell.length_b 111.239 _cell.length_c 67.292 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4P0W _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 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 OD2 ASP 98 A ASP 103 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc2 A OD1 ASP 98 A ASP 103 1_555 F MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc3 A OD2 ASP 102 A ASP 107 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc4 A OD2 ASP 102 A ASP 107 1_555 F MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc5 A OD2 ASP 238 A ASP 243 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc6 C O16 ZOL . A ZOL 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc7 C O12 ZOL . A ZOL 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc8 C O17 ZOL . A ZOL 501 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc9 C O11 ZOL . A ZOL 501 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc10 C O12 ZOL . A ZOL 501 1_555 F MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? metalc ? metalc11 D MG MG . A MG 502 1_555 G O HOH . A HOH 643 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc12 D MG MG . A MG 502 1_555 G O HOH . A HOH 644 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc13 E MG MG . A MG 503 1_555 G O HOH . A HOH 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc14 E MG MG . A MG 503 1_555 G O HOH . A HOH 622 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc15 E MG MG . A MG 503 1_555 G O HOH . A HOH 629 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc16 F MG MG . A MG 504 1_555 G O HOH . A HOH 641 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? metalc ? metalc17 F MG MG . A MG 504 1_555 G O HOH . A HOH 642 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.764 ? metalc ? metalc18 F MG MG . A MG 504 1_555 G O HOH . A HOH 647 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? # _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 429 n n O17 H17 ZOL sing 430 n n P14 O16 ZOL sing 431 n n P14 O15 ZOL doub 432 n n P14 C8 ZOL sing 433 n n O16 H1 ZOL sing 434 n n C8 P9 ZOL sing 435 n n C8 O13 ZOL sing 436 n n C8 C7 ZOL sing 437 n n P9 O10 ZOL sing 438 n n P9 O11 ZOL sing 439 n n P9 O12 ZOL doub 440 n n O10 H10 ZOL sing 441 n n O11 H11 ZOL sing 442 n n O13 H13 ZOL sing 443 n n C7 N15 ZOL sing 444 n n C7 H71 ZOL sing 445 n n C7 H72 ZOL sing 446 n n N15 C16 ZOL sing 447 n y N15 C19 ZOL sing 448 n y C16 N17 ZOL doub 449 n y C16 H16 ZOL sing 450 n n N17 C18 ZOL sing 451 n y C18 C19 ZOL doub 452 n y C18 H18 ZOL sing 453 n n C19 H19 ZOL sing 454 n n # _atom_sites.entry_id 4P0W _atom_sites.fract_transf_matrix[1][1] 0.00899 _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] 0.00899 _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] 0.014861 _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 1XH A 1 500 500 1XH 1XH . C 3 ZOL A 1 501 501 ZOL ZOL . D 4 MG A 1 502 502 MG MG . E 4 MG A 1 503 503 MG MG . F 4 MG A 1 504 504 MG MG . G 5 HOH A 1 601 375 HOH HOH . G 5 HOH A 2 602 405 HOH HOH . G 5 HOH A 3 603 388 HOH HOH . G 5 HOH A 4 604 372 HOH HOH . G 5 HOH A 5 605 360 HOH HOH . G 5 HOH A 6 606 403 HOH HOH . G 5 HOH A 7 607 366 HOH HOH . G 5 HOH A 8 608 382 HOH HOH . G 5 HOH A 9 609 387 HOH HOH . G 5 HOH A 10 610 391 HOH HOH . G 5 HOH A 11 611 369 HOH HOH . G 5 HOH A 12 612 374 HOH HOH . G 5 HOH A 13 613 386 HOH HOH . G 5 HOH A 14 614 379 HOH HOH . G 5 HOH A 15 615 413 HOH HOH . G 5 HOH A 16 616 411 HOH HOH . G 5 HOH A 17 617 384 HOH HOH . G 5 HOH A 18 618 404 HOH HOH . G 5 HOH A 19 619 356 HOH HOH . G 5 HOH A 20 620 357 HOH HOH . G 5 HOH A 21 621 358 HOH HOH . G 5 HOH A 22 622 359 HOH HOH . G 5 HOH A 23 623 362 HOH HOH . G 5 HOH A 24 624 363 HOH HOH . G 5 HOH A 25 625 364 HOH HOH . G 5 HOH A 26 626 365 HOH HOH . G 5 HOH A 27 627 367 HOH HOH . G 5 HOH A 28 628 368 HOH HOH . G 5 HOH A 29 629 370 HOH HOH . G 5 HOH A 30 630 371 HOH HOH . G 5 HOH A 31 631 373 HOH HOH . G 5 HOH A 32 632 376 HOH HOH . G 5 HOH A 33 633 377 HOH HOH . G 5 HOH A 34 634 378 HOH HOH . G 5 HOH A 35 635 380 HOH HOH . G 5 HOH A 36 636 381 HOH HOH . G 5 HOH A 37 637 383 HOH HOH . G 5 HOH A 38 638 385 HOH HOH . G 5 HOH A 39 639 389 HOH HOH . G 5 HOH A 40 640 392 HOH HOH . G 5 HOH A 41 641 393 HOH HOH . G 5 HOH A 42 642 394 HOH HOH . G 5 HOH A 43 643 395 HOH HOH . G 5 HOH A 44 644 396 HOH HOH . G 5 HOH A 45 645 397 HOH HOH . G 5 HOH A 46 646 398 HOH HOH . G 5 HOH A 47 647 399 HOH HOH . G 5 HOH A 48 648 400 HOH HOH . G 5 HOH A 49 649 401 HOH HOH . G 5 HOH A 50 650 402 HOH HOH . G 5 HOH A 51 651 406 HOH HOH . G 5 HOH A 52 652 407 HOH HOH . G 5 HOH A 53 653 408 HOH HOH . G 5 HOH A 54 654 409 HOH HOH . G 5 HOH A 55 655 410 HOH HOH . G 5 HOH A 56 656 412 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 . . . C 3 36.728 15.031 8.298 1 28.15 ? O17 ZOL 501 A 1 HETATM 2 P P14 ZOL . . . C 3 35.585 15.271 7.399 1 33.61 ? P14 ZOL 501 A 1 HETATM 3 O O16 ZOL . . . C 3 35.505 16.7 6.905 1 31.04 ? O16 ZOL 501 A 1 HETATM 4 O O15 ZOL . . . C 3 35.342 14.33 6.33 1 32.61 ? O15 ZOL 501 A 1 HETATM 5 C C8 ZOL . . . C 3 34.145 14.983 8.452 1 33.23 ? C8 ZOL 501 A 1 HETATM 6 P P9 ZOL . . . C 3 34.047 16.28 9.7 1 31.44 ? P9 ZOL 501 A 1 HETATM 7 O O10 ZOL . . . C 3 32.83 16.014 10.489 1 33.63 ? O10 ZOL 501 A 1 HETATM 8 O O11 ZOL . . . C 3 35.403 16.268 10.311 1 33.46 ? O11 ZOL 501 A 1 HETATM 9 O O12 ZOL . . . C 3 33.718 17.776 8.994 1 27.87 ? O12 ZOL 501 A 1 HETATM 10 O O13 ZOL . . . C 3 34.323 13.764 9.146 1 33.86 ? O13 ZOL 501 A 1 HETATM 11 C C7 ZOL . . . C 3 32.98 14.999 7.5 1 35.56 ? C7 ZOL 501 A 1 HETATM 12 N N15 ZOL . . . C 3 31.75 14.559 8.185 1 33.06 ? N15 ZOL 501 A 1 HETATM 13 C C16 ZOL . . . C 3 31.444 13.498 8.909 1 34.14 ? C16 ZOL 501 A 1 HETATM 14 N N17 ZOL . . . C 3 30.155 13.608 9.292 1 33.73 ? N17 ZOL 501 A 1 HETATM 15 C C18 ZOL . . . C 3 29.688 14.752 8.806 1 34.42 ? C18 ZOL 501 A 1 HETATM 16 C C19 ZOL . . . C 3 30.661 15.336 8.096 1 30.9 ? C19 ZOL 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 16 #