data_1ZW5 # _model_server_result.job_id UX-xQEHegfpLGI5H27KHeA _model_server_result.datetime_utc '2024-11-24 23:55:21' _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 1zw5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":901}' # _entry.id 1ZW5 # _exptl.entry_id 1ZW5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 272.09 _entity.id 4 _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 1ZW5 _cell.length_a 112.255 _cell.length_b 112.255 _cell.length_c 63.245 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ZW5 _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,PQS _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 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 105 A ASP 117 1_555 B MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc2 A OD1 ASP 105 A ASP 117 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc3 A OD2 ASP 105 A ASP 117 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.139 ? metalc ? metalc4 A OD2 ASP 109 A ASP 121 1_555 B MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc5 A OD2 ASP 109 A ASP 121 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc6 A OD2 ASP 245 A ASP 257 1_555 C MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc7 F O17 ZOL . A ZOL 901 1_555 B MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc8 F O11 ZOL . A ZOL 901 1_555 B MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc9 F O15 ZOL . A ZOL 901 1_555 C MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 4.608 ? metalc ? metalc10 F O12 ZOL . A ZOL 901 1_555 C MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc11 F O16 ZOL . A ZOL 901 1_555 C MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc12 F O17 ZOL . A ZOL 901 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc13 B MG MG . A MG 907 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? metalc ? metalc14 B MG MG . A MG 907 1_555 G O HOH . A HOH 911 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? metalc ? metalc15 B MG MG . A MG 907 1_555 G O HOH . A HOH 913 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc16 C MG MG . A MG 908 1_555 G O HOH . A HOH 915 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc17 C MG MG . A MG 908 1_555 G O HOH . A HOH 917 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc18 C MG MG . A MG 908 1_555 G O HOH . A HOH 960 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc19 D MG MG . A MG 909 1_555 G O HOH . A HOH 912 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc20 D MG MG . A MG 909 1_555 G O HOH . A HOH 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc21 D MG MG . A MG 909 1_555 G O HOH . A HOH 916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? # _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 401 n n O17 H17 ZOL sing 402 n n P14 O16 ZOL sing 403 n n P14 O15 ZOL doub 404 n n P14 C8 ZOL sing 405 n n O16 H1 ZOL sing 406 n n C8 P9 ZOL sing 407 n n C8 O13 ZOL sing 408 n n C8 C7 ZOL sing 409 n n P9 O10 ZOL sing 410 n n P9 O11 ZOL sing 411 n n P9 O12 ZOL doub 412 n n O10 H10 ZOL sing 413 n n O11 H11 ZOL sing 414 n n O13 H13 ZOL sing 415 n n C7 N15 ZOL sing 416 n n C7 H71 ZOL sing 417 n n C7 H72 ZOL sing 418 n n N15 C16 ZOL sing 419 n y N15 C19 ZOL sing 420 n y C16 N17 ZOL doub 421 n y C16 H16 ZOL sing 422 n n N17 C18 ZOL sing 423 n y C18 C19 ZOL doub 424 n y C18 H18 ZOL sing 425 n n C19 H19 ZOL sing 426 n n # _atom_sites.entry_id 1ZW5 _atom_sites.fract_transf_matrix[1][1] 0.008908 _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] 0.008908 _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] 0.015812 _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 1 907 907 MG MG . C 2 MG A 1 908 908 MG MG . D 2 MG A 1 909 909 MG MG . E 3 IPE A 1 900 900 IPE IPR . F 4 ZOL A 1 901 901 ZOL ZOL . G 5 HOH A 1 910 1 HOH HOH . G 5 HOH A 2 911 2 HOH HOH . G 5 HOH A 3 912 3 HOH HOH . G 5 HOH A 4 913 4 HOH HOH . G 5 HOH A 5 914 5 HOH HOH . G 5 HOH A 6 915 6 HOH HOH . G 5 HOH A 7 916 7 HOH HOH . G 5 HOH A 8 917 8 HOH HOH . G 5 HOH A 9 918 9 HOH HOH . G 5 HOH A 10 919 10 HOH HOH . G 5 HOH A 11 920 11 HOH HOH . G 5 HOH A 12 921 12 HOH HOH . G 5 HOH A 13 922 13 HOH HOH . G 5 HOH A 14 923 14 HOH HOH . G 5 HOH A 15 924 15 HOH HOH . G 5 HOH A 16 925 16 HOH HOH . G 5 HOH A 17 926 17 HOH HOH . G 5 HOH A 18 927 18 HOH HOH . G 5 HOH A 19 928 19 HOH HOH . G 5 HOH A 20 929 20 HOH HOH . G 5 HOH A 21 930 21 HOH HOH . G 5 HOH A 22 931 22 HOH HOH . G 5 HOH A 23 932 23 HOH HOH . G 5 HOH A 24 933 24 HOH HOH . G 5 HOH A 25 934 25 HOH HOH . G 5 HOH A 26 935 26 HOH HOH . G 5 HOH A 27 936 27 HOH HOH . G 5 HOH A 28 937 28 HOH HOH . G 5 HOH A 29 938 29 HOH HOH . G 5 HOH A 30 939 30 HOH HOH . G 5 HOH A 31 940 31 HOH HOH . G 5 HOH A 32 941 32 HOH HOH . G 5 HOH A 33 942 33 HOH HOH . G 5 HOH A 34 943 34 HOH HOH . G 5 HOH A 35 944 35 HOH HOH . G 5 HOH A 36 945 36 HOH HOH . G 5 HOH A 37 946 37 HOH HOH . G 5 HOH A 38 947 38 HOH HOH . G 5 HOH A 39 948 39 HOH HOH . G 5 HOH A 40 949 40 HOH HOH . G 5 HOH A 41 950 41 HOH HOH . G 5 HOH A 42 951 42 HOH HOH . G 5 HOH A 43 952 43 HOH HOH . G 5 HOH A 44 953 44 HOH HOH . G 5 HOH A 45 954 45 HOH HOH . G 5 HOH A 46 955 46 HOH HOH . G 5 HOH A 47 956 47 HOH HOH . G 5 HOH A 48 957 48 HOH HOH . G 5 HOH A 49 958 49 HOH HOH . G 5 HOH A 50 959 50 HOH HOH . G 5 HOH A 51 960 51 HOH HOH . G 5 HOH A 52 961 52 HOH HOH . G 5 HOH A 53 962 53 HOH HOH . G 5 HOH A 54 963 54 HOH HOH . G 5 HOH A 55 964 55 HOH HOH . G 5 HOH A 56 965 56 HOH HOH . G 5 HOH A 57 966 57 HOH HOH . G 5 HOH A 58 967 58 HOH HOH . G 5 HOH A 59 968 59 HOH HOH . G 5 HOH A 60 969 60 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 . . . F 4 17.348 33.943 -8.86 1 33.44 ? O17 ZOL 901 A 1 HETATM 2 P P14 ZOL . . . F 4 16.144 34.196 -9.661 1 44.34 ? P14 ZOL 901 A 1 HETATM 3 O O16 ZOL . . . F 4 16.043 35.546 -10.342 1 34.12 ? O16 ZOL 901 A 1 HETATM 4 O O15 ZOL . . . F 4 16.021 33.019 -10.636 1 30.28 ? O15 ZOL 901 A 1 HETATM 5 C C8 ZOL . . . F 4 14.954 34.29 -8.276 1 36.82 ? C8 ZOL 901 A 1 HETATM 6 P P9 ZOL . . . F 4 15.358 35.693 -7.182 1 40.91 ? P9 ZOL 901 A 1 HETATM 7 O O10 ZOL . . . F 4 14.465 35.689 -5.968 1 26.44 ? O10 ZOL 901 A 1 HETATM 8 O O11 ZOL . . . F 4 16.834 35.612 -6.737 1 35.18 ? O11 ZOL 901 A 1 HETATM 9 O O12 ZOL . . . F 4 15.042 36.909 -7.943 1 35.57 ? O12 ZOL 901 A 1 HETATM 10 O O13 ZOL . . . F 4 13.641 34.5 -8.787 1 44.02 ? O13 ZOL 901 A 1 HETATM 11 C C7 ZOL . . . F 4 14.921 33.043 -7.335 1 41.2 ? C7 ZOL 901 A 1 HETATM 12 N N15 ZOL . . . F 4 14.591 31.764 -7.984 1 38.32 ? N15 ZOL 901 A 1 HETATM 13 C C16 ZOL . . . F 4 13.713 31.557 -8.978 1 34.35 ? C16 ZOL 901 A 1 HETATM 14 N N17 ZOL . . . F 4 13.718 30.255 -9.293 1 37.12 ? N17 ZOL 901 A 1 HETATM 15 C C18 ZOL . . . F 4 14.57 29.633 -8.459 1 42.14 ? C18 ZOL 901 A 1 HETATM 16 C C19 ZOL . . . F 4 15.124 30.585 -7.644 1 32.62 ? C19 ZOL 901 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 443 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 16 #