data_3N46 # _model_server_result.job_id R4kAGldZgbPFH0G7o_w6TQ _model_server_result.datetime_utc '2024-10-19 15:24:59' _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 3n46 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":354}' # _entry.id 3N46 # _exptl.entry_id 3N46 _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 3N46 _cell.length_a 110.853 _cell.length_b 110.853 _cell.length_c 70.861 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3N46 _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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 110.853 110.853 35.4305 # _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 E MG MG . F MG 2 1_555 A OD2 ASP 240 F ASP 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc2 E MG MG . F MG 2 1_555 C O12 ZOL . F ZOL 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc3 E MG MG . F MG 2 1_555 C O17 ZOL . F ZOL 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc4 E MG MG . F MG 2 1_555 H O HOH . F HOH 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc5 E MG MG . F MG 2 1_555 H O HOH . F HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc6 E MG MG . F MG 2 1_555 H O HOH . F HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc7 F MG MG . F MG 3 1_555 A OD2 ASP 100 F ASP 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc8 F MG MG . F MG 3 1_555 A OD2 ASP 104 F ASP 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc9 F MG MG . F MG 3 1_555 C O11 ZOL . F ZOL 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc10 F MG MG . F MG 3 1_555 H O HOH . F HOH 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc11 F MG MG . F MG 3 1_555 H O HOH . F HOH 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc12 F MG MG . F MG 3 1_555 H O HOH . F HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc13 A OD1 ASP 100 F ASP 103 1_555 D MG MG . F MG 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc14 A OD2 ASP 104 F ASP 107 1_555 D MG MG . F MG 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc15 C O15 ZOL . F ZOL 354 1_555 D MG MG . F MG 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc16 C O11 ZOL . F ZOL 354 1_555 D MG MG . F MG 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc17 D MG MG . F MG 355 1_555 H O HOH . F HOH 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc18 D MG MG . F MG 355 1_555 H O HOH . F HOH 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? # _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 419 n n O17 H17 ZOL sing 420 n n P14 O16 ZOL sing 421 n n P14 O15 ZOL doub 422 n n P14 C8 ZOL sing 423 n n O16 H1 ZOL sing 424 n n C8 P9 ZOL sing 425 n n C8 O13 ZOL sing 426 n n C8 C7 ZOL sing 427 n n P9 O10 ZOL sing 428 n n P9 O11 ZOL sing 429 n n P9 O12 ZOL doub 430 n n O10 H10 ZOL sing 431 n n O11 H11 ZOL sing 432 n n O13 H13 ZOL sing 433 n n C7 N15 ZOL sing 434 n n C7 H71 ZOL sing 435 n n C7 H72 ZOL sing 436 n n N15 C16 ZOL sing 437 n y N15 C19 ZOL sing 438 n y C16 N17 ZOL doub 439 n y C16 H16 ZOL sing 440 n n N17 C18 ZOL sing 441 n y C18 C19 ZOL doub 442 n y C18 H18 ZOL sing 443 n n C19 H19 ZOL sing 444 n n # _atom_sites.entry_id 3N46 _atom_sites.fract_transf_matrix[1][1] 0.009021 _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] 0.009021 _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] 0.014112 _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 3N5 F 1 1 1 3N5 3N5 . C 3 ZOL F 1 354 1 ZOL ZOL . D 4 MG F 1 355 1 MG MG . E 4 MG F 1 2 2 MG MG . F 4 MG F 1 3 3 MG MG . G 5 PO4 F 1 356 1 PO4 PO4 . H 6 HOH F 1 357 1 HOH HOH . H 6 HOH F 2 358 2 HOH HOH . H 6 HOH F 3 359 3 HOH HOH . H 6 HOH F 4 360 4 HOH HOH . H 6 HOH F 5 361 5 HOH HOH . H 6 HOH F 6 362 6 HOH HOH . H 6 HOH F 7 363 7 HOH HOH . H 6 HOH F 8 364 8 HOH HOH . H 6 HOH F 9 365 9 HOH HOH . H 6 HOH F 10 366 10 HOH HOH . H 6 HOH F 11 367 11 HOH HOH . H 6 HOH F 12 368 12 HOH HOH . H 6 HOH F 13 369 13 HOH HOH . H 6 HOH F 14 370 14 HOH HOH . H 6 HOH F 15 371 15 HOH HOH . H 6 HOH F 16 372 16 HOH HOH . H 6 HOH F 17 373 17 HOH HOH . H 6 HOH F 18 374 18 HOH HOH . H 6 HOH F 19 375 19 HOH HOH . H 6 HOH F 20 376 20 HOH HOH . H 6 HOH F 21 377 21 HOH HOH . H 6 HOH F 22 378 22 HOH HOH . H 6 HOH F 23 379 23 HOH HOH . H 6 HOH F 24 380 24 HOH HOH . H 6 HOH F 25 381 25 HOH HOH . H 6 HOH F 26 382 26 HOH HOH . H 6 HOH F 27 383 27 HOH HOH . H 6 HOH F 28 384 28 HOH HOH . H 6 HOH F 29 385 29 HOH HOH . H 6 HOH F 30 386 30 HOH HOH . H 6 HOH F 31 387 31 HOH HOH . H 6 HOH F 32 388 32 HOH HOH . H 6 HOH F 33 389 33 HOH HOH . H 6 HOH F 34 390 34 HOH HOH . H 6 HOH F 35 391 35 HOH HOH . H 6 HOH F 36 392 36 HOH HOH . H 6 HOH F 37 393 37 HOH HOH . H 6 HOH F 38 394 38 HOH HOH . H 6 HOH F 39 395 39 HOH HOH . H 6 HOH F 40 396 40 HOH HOH . H 6 HOH F 41 397 41 HOH HOH . H 6 HOH F 42 398 42 HOH HOH . H 6 HOH F 43 399 43 HOH HOH . H 6 HOH F 44 400 44 HOH HOH . H 6 HOH F 45 401 45 HOH HOH . H 6 HOH F 46 402 46 HOH HOH . H 6 HOH F 47 403 47 HOH HOH . H 6 HOH F 48 404 48 HOH HOH . H 6 HOH F 49 405 49 HOH HOH . H 6 HOH F 50 406 50 HOH HOH . H 6 HOH F 51 407 51 HOH HOH . H 6 HOH F 52 408 52 HOH HOH . H 6 HOH F 53 409 53 HOH HOH . H 6 HOH F 54 410 54 HOH HOH . H 6 HOH F 55 411 55 HOH HOH . H 6 HOH F 56 412 56 HOH HOH . H 6 HOH F 57 413 57 HOH HOH . H 6 HOH F 58 414 58 HOH HOH . H 6 HOH F 59 415 59 HOH HOH . H 6 HOH F 60 416 60 HOH HOH . H 6 HOH F 61 417 61 HOH HOH . H 6 HOH F 62 418 62 HOH HOH . H 6 HOH F 63 419 63 HOH HOH . H 6 HOH F 64 420 64 HOH HOH . H 6 HOH F 65 421 65 HOH HOH . H 6 HOH F 66 422 66 HOH HOH . H 6 HOH F 67 423 67 HOH HOH . H 6 HOH F 68 424 68 HOH HOH . H 6 HOH F 69 425 69 HOH HOH . H 6 HOH F 70 426 70 HOH HOH . H 6 HOH F 71 427 71 HOH HOH . H 6 HOH F 72 428 72 HOH HOH . H 6 HOH F 73 429 73 HOH HOH . H 6 HOH F 74 430 74 HOH HOH . H 6 HOH F 75 431 75 HOH HOH . H 6 HOH F 76 432 76 HOH HOH . H 6 HOH F 77 433 77 HOH HOH . H 6 HOH F 78 434 78 HOH HOH . H 6 HOH F 79 435 79 HOH HOH . H 6 HOH F 80 436 80 HOH HOH . H 6 HOH F 81 437 81 HOH HOH . H 6 HOH F 82 438 82 HOH HOH . H 6 HOH F 83 439 83 HOH HOH . H 6 HOH F 84 440 84 HOH HOH . H 6 HOH F 85 441 85 HOH HOH . H 6 HOH F 86 442 86 HOH HOH . H 6 HOH F 87 443 87 HOH HOH . H 6 HOH F 88 444 88 HOH HOH . H 6 HOH F 89 445 89 HOH HOH . H 6 HOH F 90 446 90 HOH HOH . H 6 HOH F 91 447 91 HOH HOH . H 6 HOH F 92 448 92 HOH HOH . H 6 HOH F 93 449 93 HOH HOH . H 6 HOH F 94 450 94 HOH HOH . H 6 HOH F 95 451 95 HOH HOH . H 6 HOH F 96 452 96 HOH HOH . H 6 HOH F 97 453 97 HOH HOH . H 6 HOH F 98 454 98 HOH HOH . H 6 HOH F 99 455 99 HOH HOH . H 6 HOH F 100 456 100 HOH HOH . H 6 HOH F 101 457 101 HOH HOH . H 6 HOH F 102 458 102 HOH HOH . H 6 HOH F 103 459 103 HOH HOH . H 6 HOH F 104 460 104 HOH HOH . H 6 HOH F 105 461 105 HOH HOH . H 6 HOH F 106 462 106 HOH HOH . H 6 HOH F 107 463 107 HOH HOH . H 6 HOH F 108 464 108 HOH HOH . H 6 HOH F 109 465 109 HOH HOH . H 6 HOH F 110 466 110 HOH HOH . H 6 HOH F 111 467 111 HOH HOH . H 6 HOH F 112 468 112 HOH HOH . H 6 HOH F 113 469 113 HOH HOH . H 6 HOH F 114 470 114 HOH HOH . H 6 HOH F 115 471 115 HOH HOH . H 6 HOH F 116 472 116 HOH HOH . H 6 HOH F 117 473 117 HOH HOH . H 6 HOH F 118 474 118 HOH HOH . H 6 HOH F 119 475 119 HOH HOH . H 6 HOH F 120 476 120 HOH HOH . H 6 HOH F 121 477 121 HOH HOH . H 6 HOH F 122 478 122 HOH HOH . H 6 HOH F 123 479 123 HOH HOH . H 6 HOH F 124 480 124 HOH HOH . H 6 HOH F 125 481 125 HOH HOH . H 6 HOH F 126 482 126 HOH HOH . H 6 HOH F 127 483 127 HOH HOH . H 6 HOH F 128 484 128 HOH HOH . H 6 HOH F 129 485 129 HOH HOH . H 6 HOH F 130 486 130 HOH HOH . H 6 HOH F 131 487 131 HOH HOH . H 6 HOH F 132 488 132 HOH HOH . H 6 HOH F 133 489 133 HOH HOH . H 6 HOH F 134 490 134 HOH HOH . H 6 HOH F 135 491 135 HOH HOH . H 6 HOH F 136 492 136 HOH HOH . H 6 HOH F 137 493 137 HOH HOH . H 6 HOH F 138 494 138 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 15.553 73.629 26.546 1 42.28 ? O17 ZOL 354 F 1 HETATM 2 P P14 ZOL . . . C 3 15.693 74.896 25.584 1 46.07 ? P14 ZOL 354 F 1 HETATM 3 O O16 ZOL . . . C 3 14.423 74.94 24.594 1 47.78 ? O16 ZOL 354 F 1 HETATM 4 O O15 ZOL . . . C 3 17.018 74.953 24.892 1 47.99 ? O15 ZOL 354 F 1 HETATM 5 C C8 ZOL . . . C 3 15.371 76.417 26.584 1 44.89 ? C8 ZOL 354 F 1 HETATM 6 P P9 ZOL . . . C 3 16.765 76.515 27.79 1 45.49 ? P9 ZOL 354 F 1 HETATM 7 O O10 ZOL . . . C 3 16.39 77.765 28.711 1 48.68 ? O10 ZOL 354 F 1 HETATM 8 O O11 ZOL . . . C 3 18.131 76.591 27.173 1 47.29 ? O11 ZOL 354 F 1 HETATM 9 O O12 ZOL . . . C 3 16.551 75.207 28.649 1 44.92 ? O12 ZOL 354 F 1 HETATM 10 O O13 ZOL . . . C 3 14.127 76.305 27.282 1 42.32 ? O13 ZOL 354 F 1 HETATM 11 C C7 ZOL . . . C 3 15.287 77.601 25.574 1 38.49 ? C7 ZOL 354 F 1 HETATM 12 N N15 ZOL . . . C 3 15.075 78.866 26.245 1 38.44 ? N15 ZOL 354 F 1 HETATM 13 C C16 ZOL . . . C 3 14.211 79.109 27.138 1 35.43 ? C16 ZOL 354 F 1 HETATM 14 N N17 ZOL . . . C 3 14.317 80.292 27.49 1 35.96 ? N17 ZOL 354 F 1 HETATM 15 C C18 ZOL . . . C 3 15.234 80.936 26.865 1 30.28 ? C18 ZOL 354 F 1 HETATM 16 C C19 ZOL . . . C 3 15.759 79.982 26.028 1 36.54 ? C19 ZOL 354 F 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 16 #