data_2F9K # _model_server_result.job_id aO6K4WLSyikRk0RmieyqsA _model_server_result.datetime_utc '2024-11-05 21:19:17' _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 2f9k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":9001}' # _entry.id 2F9K # _exptl.entry_id 2F9K _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 2F9K _cell.length_a 111.27 _cell.length_b 111.27 _cell.length_c 69.029 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2F9K _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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 111.27 111.27 34.5145 # _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 OD1 ASP 100 F ASP 103 1_555 B ZN ZN . F ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc2 A OD2 ASP 100 F ASP 103 1_555 D ZN ZN . F ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc3 A OD2 ASP 104 F ASP 107 1_555 B ZN ZN . F ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc4 A OD2 ASP 104 F ASP 107 1_555 D ZN ZN . F ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc5 A OD2 ASP 240 F ASP 243 1_555 C ZN ZN . F ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc6 B ZN ZN . F ZN 1001 1_555 F O17 ZOL . F ZOL 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc7 B ZN ZN . F ZN 1001 1_555 F O12 ZOL . F ZOL 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc8 B ZN ZN . F ZN 1001 1_555 G O HOH . F HOH 9006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc9 B ZN ZN . F ZN 1001 1_555 G O HOH . F HOH 9016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? metalc ? metalc10 C ZN ZN . F ZN 1002 1_555 F O16 ZOL . F ZOL 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc11 C ZN ZN . F ZN 1002 1_555 F O11 ZOL . F ZOL 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc12 C ZN ZN . F ZN 1002 1_555 G O HOH . F HOH 9005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc13 C ZN ZN . F ZN 1002 1_555 G O HOH . F HOH 9014 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc14 C ZN ZN . F ZN 1002 1_555 G O HOH . F HOH 9020 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc15 D ZN ZN . F ZN 1003 1_555 F O12 ZOL . F ZOL 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc16 D ZN ZN . F ZN 1003 1_555 G O HOH . F HOH 9007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc17 D ZN ZN . F ZN 1003 1_555 G O HOH . F HOH 9008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc18 D ZN ZN . F ZN 1003 1_555 G O HOH . F HOH 9017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? # _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 380 n n O17 H17 ZOL sing 381 n n P14 O16 ZOL sing 382 n n P14 O15 ZOL doub 383 n n P14 C8 ZOL sing 384 n n O16 H1 ZOL sing 385 n n C8 P9 ZOL sing 386 n n C8 O13 ZOL sing 387 n n C8 C7 ZOL sing 388 n n P9 O10 ZOL sing 389 n n P9 O11 ZOL sing 390 n n P9 O12 ZOL doub 391 n n O10 H10 ZOL sing 392 n n O11 H11 ZOL sing 393 n n O13 H13 ZOL sing 394 n n C7 N15 ZOL sing 395 n n C7 H71 ZOL sing 396 n n C7 H72 ZOL sing 397 n n N15 C16 ZOL sing 398 n y N15 C19 ZOL sing 399 n y C16 N17 ZOL doub 400 n y C16 H16 ZOL sing 401 n n N17 C18 ZOL sing 402 n y C18 C19 ZOL doub 403 n y C18 H18 ZOL sing 404 n n C19 H19 ZOL sing 405 n n # _atom_sites.entry_id 2F9K _atom_sites.fract_transf_matrix[1][1] 0.008987 _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] 0.008987 _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] 0.014487 _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 ZN F 1 1001 1001 ZN ZN . C 2 ZN F 1 1002 1002 ZN ZN . D 2 ZN F 1 1003 1003 ZN ZN . E 3 PO4 F 1 5001 5001 PO4 PO4 . F 4 ZOL F 1 9001 9001 ZOL ZOL . G 5 HOH F 1 9002 1 HOH HOH . G 5 HOH F 2 9003 2 HOH HOH . G 5 HOH F 3 9004 3 HOH HOH . G 5 HOH F 4 9005 4 HOH HOH . G 5 HOH F 5 9006 5 HOH HOH . G 5 HOH F 6 9007 6 HOH HOH . G 5 HOH F 7 9008 7 HOH HOH . G 5 HOH F 8 9009 8 HOH HOH . G 5 HOH F 9 9010 9 HOH HOH . G 5 HOH F 10 9011 10 HOH HOH . G 5 HOH F 11 9012 11 HOH HOH . G 5 HOH F 12 9013 12 HOH HOH . G 5 HOH F 13 9014 13 HOH HOH . G 5 HOH F 14 9015 14 HOH HOH . G 5 HOH F 15 9016 15 HOH HOH . G 5 HOH F 16 9017 16 HOH HOH . G 5 HOH F 17 9018 17 HOH HOH . G 5 HOH F 18 9019 18 HOH HOH . G 5 HOH F 19 9020 19 HOH HOH . G 5 HOH F 20 9021 20 HOH HOH . G 5 HOH F 21 9022 21 HOH HOH . G 5 HOH F 22 9023 22 HOH HOH . G 5 HOH F 23 9024 23 HOH HOH . G 5 HOH F 24 9025 24 HOH HOH . G 5 HOH F 25 9026 25 HOH HOH . G 5 HOH F 26 9027 26 HOH HOH . G 5 HOH F 27 9028 27 HOH HOH . G 5 HOH F 28 9029 28 HOH HOH . G 5 HOH F 29 9030 29 HOH HOH . G 5 HOH F 30 9031 30 HOH HOH . G 5 HOH F 31 9032 31 HOH HOH . G 5 HOH F 32 9033 32 HOH HOH . G 5 HOH F 33 9034 33 HOH HOH . G 5 HOH F 34 9035 34 HOH HOH . G 5 HOH F 35 9036 35 HOH HOH . G 5 HOH F 36 9037 36 HOH HOH . G 5 HOH F 37 9038 37 HOH HOH . G 5 HOH F 38 9039 38 HOH HOH . G 5 HOH F 39 9040 39 HOH HOH . G 5 HOH F 40 9041 40 HOH HOH . G 5 HOH F 41 9042 41 HOH HOH . G 5 HOH F 42 9043 42 HOH HOH . G 5 HOH F 43 9044 43 HOH HOH . G 5 HOH F 44 9045 44 HOH HOH . G 5 HOH F 45 9046 45 HOH HOH . G 5 HOH F 46 9047 46 HOH HOH . G 5 HOH F 47 9048 47 HOH HOH . G 5 HOH F 48 9049 48 HOH HOH . G 5 HOH F 49 9050 49 HOH HOH . G 5 HOH F 50 9051 50 HOH HOH . G 5 HOH F 51 9052 51 HOH HOH . G 5 HOH F 52 9053 52 HOH HOH . G 5 HOH F 53 9054 53 HOH HOH . G 5 HOH F 54 9055 54 HOH HOH . G 5 HOH F 55 9056 55 HOH HOH . G 5 HOH F 56 9057 56 HOH HOH . G 5 HOH F 57 9058 57 HOH HOH . G 5 HOH F 58 9059 58 HOH HOH . G 5 HOH F 59 9060 59 HOH HOH . G 5 HOH F 60 9061 60 HOH HOH . G 5 HOH F 61 9062 61 HOH HOH . G 5 HOH F 62 9063 62 HOH HOH . G 5 HOH F 63 9064 63 HOH HOH . G 5 HOH F 64 9065 64 HOH HOH . G 5 HOH F 65 9066 65 HOH HOH . G 5 HOH F 66 9067 66 HOH HOH . G 5 HOH F 67 9068 67 HOH HOH . G 5 HOH F 68 9069 68 HOH HOH . G 5 HOH F 69 9070 69 HOH HOH . G 5 HOH F 70 9071 70 HOH HOH . G 5 HOH F 71 9072 71 HOH HOH . G 5 HOH F 72 9073 72 HOH HOH . G 5 HOH F 73 9074 73 HOH HOH . G 5 HOH F 74 9075 74 HOH HOH . G 5 HOH F 75 9076 75 HOH HOH . G 5 HOH F 76 9077 76 HOH HOH . G 5 HOH F 77 9078 77 HOH HOH . G 5 HOH F 78 9079 78 HOH HOH . G 5 HOH F 79 9080 79 HOH HOH . G 5 HOH F 80 9081 80 HOH HOH . G 5 HOH F 81 9082 81 HOH HOH . G 5 HOH F 82 9083 82 HOH HOH . G 5 HOH F 83 9084 83 HOH HOH . G 5 HOH F 84 9085 84 HOH HOH . G 5 HOH F 85 9086 85 HOH HOH . G 5 HOH F 86 9087 86 HOH HOH . G 5 HOH F 87 9088 87 HOH HOH . G 5 HOH F 88 9089 88 HOH HOH . G 5 HOH F 89 9090 89 HOH HOH . G 5 HOH F 90 9091 90 HOH HOH . G 5 HOH F 91 9092 91 HOH HOH . G 5 HOH F 92 9093 92 HOH HOH . G 5 HOH F 93 9094 93 HOH HOH . G 5 HOH F 94 9095 94 HOH HOH . G 5 HOH F 95 9096 95 HOH HOH . G 5 HOH F 96 9097 96 HOH HOH . G 5 HOH F 97 9098 97 HOH HOH . G 5 HOH F 98 9099 98 HOH HOH . G 5 HOH F 99 9100 99 HOH HOH . G 5 HOH F 100 9101 100 HOH HOH . G 5 HOH F 101 9102 101 HOH HOH . G 5 HOH F 102 9103 102 HOH HOH . G 5 HOH F 103 9104 103 HOH HOH . G 5 HOH F 104 9105 104 HOH HOH . G 5 HOH F 105 9106 105 HOH HOH . G 5 HOH F 106 9107 106 HOH HOH . G 5 HOH F 107 9108 107 HOH HOH . G 5 HOH F 108 9109 108 HOH HOH . G 5 HOH F 109 9110 109 HOH HOH . G 5 HOH F 110 9111 110 HOH HOH . G 5 HOH F 111 9112 111 HOH HOH . G 5 HOH F 112 9113 112 HOH HOH . G 5 HOH F 113 9114 113 HOH HOH . G 5 HOH F 114 9115 114 HOH HOH . G 5 HOH F 115 9116 115 HOH HOH . G 5 HOH F 116 9117 116 HOH HOH . G 5 HOH F 117 9118 117 HOH HOH . G 5 HOH F 118 9119 118 HOH HOH . G 5 HOH F 119 9120 119 HOH HOH . G 5 HOH F 120 9121 120 HOH HOH . G 5 HOH F 121 9122 121 HOH HOH . G 5 HOH F 122 9123 122 HOH HOH . G 5 HOH F 123 9124 123 HOH HOH . G 5 HOH F 124 9125 124 HOH HOH . G 5 HOH F 125 9126 125 HOH HOH . G 5 HOH F 126 9127 126 HOH HOH . G 5 HOH F 127 9128 127 HOH HOH . G 5 HOH F 128 9129 128 HOH HOH . G 5 HOH F 129 9130 129 HOH HOH . G 5 HOH F 130 9131 130 HOH HOH . G 5 HOH F 131 9132 131 HOH HOH . G 5 HOH F 132 9133 132 HOH HOH . G 5 HOH F 133 9134 133 HOH HOH . G 5 HOH F 134 9135 134 HOH HOH . G 5 HOH F 135 9136 135 HOH HOH . G 5 HOH F 136 9137 136 HOH HOH . G 5 HOH F 137 9138 137 HOH HOH . G 5 HOH F 138 9139 138 HOH HOH . G 5 HOH F 139 9140 139 HOH HOH . G 5 HOH F 140 9141 140 HOH HOH . G 5 HOH F 141 9142 141 HOH HOH . G 5 HOH F 142 9143 142 HOH HOH . G 5 HOH F 143 9144 143 HOH HOH . G 5 HOH F 144 9145 144 HOH HOH . G 5 HOH F 145 9146 145 HOH HOH . G 5 HOH F 146 9147 146 HOH HOH . G 5 HOH F 147 9148 147 HOH HOH . G 5 HOH F 148 9149 148 HOH HOH . G 5 HOH F 149 9150 149 HOH HOH . G 5 HOH F 150 9151 150 HOH HOH . G 5 HOH F 151 9152 151 HOH HOH . G 5 HOH F 152 9153 152 HOH HOH . G 5 HOH F 153 9154 153 HOH HOH . G 5 HOH F 154 9155 154 HOH HOH . G 5 HOH F 155 9156 155 HOH HOH . G 5 HOH F 156 9157 156 HOH HOH . G 5 HOH F 157 9158 157 HOH HOH . G 5 HOH F 158 9159 158 HOH HOH . G 5 HOH F 159 9160 159 HOH HOH . G 5 HOH F 160 9161 160 HOH HOH . G 5 HOH F 161 9162 161 HOH HOH . G 5 HOH F 162 9163 162 HOH HOH . G 5 HOH F 163 9164 163 HOH HOH . G 5 HOH F 164 9165 164 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 16.678 75.621 24.176 1 34.18 ? O17 ZOL 9001 F 1 HETATM 2 P P14 ZOL . . . F 4 15.322 75.581 24.789 1 31.32 ? P14 ZOL 9001 F 1 HETATM 3 O O16 ZOL . . . F 4 15.124 74.277 25.668 1 24.19 ? O16 ZOL 9001 F 1 HETATM 4 O O15 ZOL . . . F 4 14.13 75.557 23.733 1 26.91 ? O15 ZOL 9001 F 1 HETATM 5 C C8 ZOL . . . F 4 15.021 77.02 25.867 1 30.93 ? C8 ZOL 9001 F 1 HETATM 6 P P9 ZOL . . . F 4 16.38 77.124 27.07 1 30.01 ? P9 ZOL 9001 F 1 HETATM 7 O O10 ZOL . . . F 4 16.006 78.329 28.057 1 28.3 ? O10 ZOL 9001 F 1 HETATM 8 O O11 ZOL . . . F 4 16.2 75.834 27.979 1 31.84 ? O11 ZOL 9001 F 1 HETATM 9 O O12 ZOL . . . F 4 17.726 77.205 26.452 1 31.8 ? O12 ZOL 9001 F 1 HETATM 10 O O13 ZOL . . . F 4 13.775 76.8 26.549 1 34.12 ? O13 ZOL 9001 F 1 HETATM 11 C C7 ZOL . . . F 4 14.961 78.285 24.96 1 32.64 ? C7 ZOL 9001 F 1 HETATM 12 N N15 ZOL . . . F 4 14.685 79.574 25.598 1 32.6 ? N15 ZOL 9001 F 1 HETATM 13 C C16 ZOL . . . F 4 13.65 79.879 26.332 1 29.93 ? C16 ZOL 9001 F 1 HETATM 14 N N17 ZOL . . . F 4 13.743 81.072 26.694 1 31.93 ? N17 ZOL 9001 F 1 HETATM 15 C C18 ZOL . . . F 4 14.948 81.667 26.173 1 32.45 ? C18 ZOL 9001 F 1 HETATM 16 C C19 ZOL . . . F 4 15.48 80.627 25.492 1 32.72 ? C19 ZOL 9001 F 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 211 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 16 #