data_4P0V # _model_server_result.job_id YjUUyV-nyUPS_nMCD4_fBA _model_server_result.datetime_utc '2024-12-26 16:01:25' _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 4p0v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4P0V # _exptl.entry_id 4P0V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 272.09 _entity.id 2 _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 4P0V _cell.length_a 112.143 _cell.length_b 112.143 _cell.length_c 67.053 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4P0V _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 -33.5265 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 97 A ASP 103 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc2 A OD1 ASP 97 A ASP 103 1_555 F MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc3 A OD2 ASP 101 A ASP 107 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc4 A OD2 ASP 101 A ASP 107 1_555 F MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc5 A OD2 ASP 237 A ASP 243 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc6 B O16 ZOL . A ZOL 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc7 B O12 ZOL . A ZOL 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc8 B O17 ZOL . A ZOL 401 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc9 B O11 ZOL . A ZOL 401 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc10 B O12 ZOL . A ZOL 401 1_555 F MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc11 D MG MG . A MG 403 1_555 G O HOH . A HOH 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc12 E MG MG . A MG 404 1_555 G O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? # _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 427 n n O17 H17 ZOL sing 428 n n P14 O16 ZOL sing 429 n n P14 O15 ZOL doub 430 n n P14 C8 ZOL sing 431 n n O16 H1 ZOL sing 432 n n C8 P9 ZOL sing 433 n n C8 O13 ZOL sing 434 n n C8 C7 ZOL sing 435 n n P9 O10 ZOL sing 436 n n P9 O11 ZOL sing 437 n n P9 O12 ZOL doub 438 n n O10 H10 ZOL sing 439 n n O11 H11 ZOL sing 440 n n O13 H13 ZOL sing 441 n n C7 N15 ZOL sing 442 n n C7 H71 ZOL sing 443 n n C7 H72 ZOL sing 444 n n N15 C16 ZOL sing 445 n y N15 C19 ZOL sing 446 n y C16 N17 ZOL doub 447 n y C16 H16 ZOL sing 448 n n N17 C18 ZOL sing 449 n y C18 C19 ZOL doub 450 n y C18 H18 ZOL sing 451 n n C19 H19 ZOL sing 452 n n # _atom_sites.entry_id 4P0V _atom_sites.fract_transf_matrix[1][1] 0.008917 _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] 0.008917 _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] 0.014914 _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 ZOL A 1 401 354 ZOL ZOL . C 3 1WO A 1 402 355 1WO NCI . D 4 MG A 1 403 356 MG MG . E 4 MG A 1 404 357 MG MG . F 4 MG A 1 405 358 MG MG . G 5 HOH A 1 501 523 HOH HOH . G 5 HOH A 2 502 509 HOH HOH . G 5 HOH A 3 503 526 HOH HOH . G 5 HOH A 4 504 515 HOH HOH . G 5 HOH A 5 505 502 HOH HOH . G 5 HOH A 6 506 528 HOH HOH . G 5 HOH A 7 507 500 HOH HOH . G 5 HOH A 8 508 501 HOH HOH . G 5 HOH A 9 509 503 HOH HOH . G 5 HOH A 10 510 504 HOH HOH . G 5 HOH A 11 511 505 HOH HOH . G 5 HOH A 12 512 506 HOH HOH . G 5 HOH A 13 513 507 HOH HOH . G 5 HOH A 14 514 508 HOH HOH . G 5 HOH A 15 515 510 HOH HOH . G 5 HOH A 16 516 511 HOH HOH . G 5 HOH A 17 517 512 HOH HOH . G 5 HOH A 18 518 513 HOH HOH . G 5 HOH A 19 519 514 HOH HOH . G 5 HOH A 20 520 516 HOH HOH . G 5 HOH A 21 521 517 HOH HOH . G 5 HOH A 22 522 518 HOH HOH . G 5 HOH A 23 523 519 HOH HOH . G 5 HOH A 24 524 520 HOH HOH . G 5 HOH A 25 525 521 HOH HOH . G 5 HOH A 26 526 522 HOH HOH . G 5 HOH A 27 527 524 HOH HOH . G 5 HOH A 28 528 525 HOH HOH . G 5 HOH A 29 529 527 HOH HOH . G 5 HOH A 30 530 529 HOH HOH . G 5 HOH A 31 531 530 HOH HOH . G 5 HOH A 32 532 531 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 . . . B 2 -15.364 37.009 -8.386 1 39.49 ? O17 ZOL 401 A 1 HETATM 2 P P14 ZOL . . . B 2 -15.454 35.978 -9.481 1 41.41 ? P14 ZOL 401 A 1 HETATM 3 O O16 ZOL . . . B 2 -16.786 35.779 -9.987 1 38.83 ? O16 ZOL 401 A 1 HETATM 4 O O15 ZOL . . . B 2 -14.425 35.881 -10.539 1 39.58 ? O15 ZOL 401 A 1 HETATM 5 C C8 ZOL . . . B 2 -15.183 34.496 -8.426 1 41.47 ? C8 ZOL 401 A 1 HETATM 6 P P9 ZOL . . . B 2 -16.533 34.322 -7.115 1 37.95 ? P9 ZOL 401 A 1 HETATM 7 O O10 ZOL . . . B 2 -16.252 33.092 -6.358 1 39.75 ? O10 ZOL 401 A 1 HETATM 8 O O11 ZOL . . . B 2 -16.471 35.612 -6.421 1 43.44 ? O11 ZOL 401 A 1 HETATM 9 O O12 ZOL . . . B 2 -17.929 34.269 -8.002 1 36.16 ? O12 ZOL 401 A 1 HETATM 10 O O13 ZOL . . . B 2 -13.967 34.697 -7.714 1 40.29 ? O13 ZOL 401 A 1 HETATM 11 C C7 ZOL . . . B 2 -15.057 33.337 -9.382 1 41.86 ? C7 ZOL 401 A 1 HETATM 12 N N15 ZOL . . . B 2 -14.751 32.046 -8.64 1 40.05 ? N15 ZOL 401 A 1 HETATM 13 C C16 ZOL . . . B 2 -13.723 31.706 -7.889 1 39.93 ? C16 ZOL 401 A 1 HETATM 14 N N17 ZOL . . . B 2 -13.883 30.437 -7.499 1 41.57 ? N17 ZOL 401 A 1 HETATM 15 C C18 ZOL . . . B 2 -15.028 29.996 -8 1 37.59 ? C18 ZOL 401 A 1 HETATM 16 C C19 ZOL . . . B 2 -15.537 30.974 -8.743 1 36.7 ? C19 ZOL 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 16 #