data_6HDW # _model_server_result.job_id -cahj9mCQg7ZoGXQI8XU-w _model_server_result.datetime_utc '2024-11-14 18:50:14' _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 6hdw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1001}' # _entry.id 6HDW # _exptl.entry_id 6HDW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 433.31 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 2-methyl-2-oxidanyl-propanoate' _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 6HDW _cell.length_a 83.871 _cell.length_b 83.871 _cell.length_c 219.811 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6HDW _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 software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C14 H20 N5 O9 P' _chem_comp.formula_weight 433.31 _chem_comp.id 8LE _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 2-methyl-2-oxidanyl-propanoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 OAE PBC 8LE doub 1 n n OAI PBC 8LE sing 2 n n PBC O5' 8LE sing 3 n n PBC OAQ 8LE sing 4 n n O5' C5' 8LE sing 5 n n OAQ CAS 8LE sing 6 n n CAA CAZ 8LE sing 7 n n C5' C4' 8LE sing 8 n n CAS OAD 8LE doub 9 n n CAS CAZ 8LE sing 10 n n C4' C3' 8LE sing 11 n n C4' O4' 8LE sing 12 n n O3' C3' 8LE sing 13 n n CAZ OAF 8LE sing 14 n n CAZ CAB 8LE sing 15 n n C3' C2' 8LE sing 16 n n O4' C1' 8LE sing 17 n n O2' C2' 8LE sing 18 n n C2' C1' 8LE sing 19 n n C1' N9 8LE sing 20 n n C8 N9 8LE sing 21 n y C8 N7 8LE doub 22 n y N9 C4 8LE sing 23 n y N7 C5 8LE sing 24 n y C4 C5 8LE doub 25 n y C4 N3 8LE sing 26 n y C5 C6 8LE sing 27 n y N3 C2 8LE doub 28 n y C6 N6 8LE sing 29 n n C6 N1 8LE doub 30 n y C2 N1 8LE sing 31 n y C2 H1 8LE sing 32 n n CAA H2 8LE sing 33 n n CAA H3 8LE sing 34 n n CAA H4 8LE sing 35 n n CAB H5 8LE sing 36 n n CAB H6 8LE sing 37 n n CAB H7 8LE sing 38 n n OAF H8 8LE sing 39 n n OAI H9 8LE sing 40 n n C5' H10 8LE sing 41 n n C5' H11 8LE sing 42 n n C4' H12 8LE sing 43 n n C3' H13 8LE sing 44 n n O3' H14 8LE sing 45 n n C2' H15 8LE sing 46 n n O2' H16 8LE sing 47 n n C1' H17 8LE sing 48 n n C8 H18 8LE sing 49 n n N6 H19 8LE sing 50 n n N6 H20 8LE sing 51 n n # _atom_sites.entry_id 6HDW _atom_sites.fract_transf_matrix[1][1] 0.011923 _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] 0.011923 _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] 0.004549 _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 8LE A 1 1001 1001 8LE 8LE . C 3 SO4 A 1 1002 1002 SO4 SO4 . D 3 SO4 A 1 1003 1003 SO4 SO4 . E 3 SO4 A 1 1004 1004 SO4 SO4 . F 4 HOH A 1 1101 1101 HOH HOH . F 4 HOH A 2 1102 1102 HOH HOH . F 4 HOH A 3 1103 1103 HOH HOH . F 4 HOH A 4 1104 1104 HOH HOH . F 4 HOH A 5 1105 1105 HOH HOH . F 4 HOH A 6 1106 1106 HOH HOH . F 4 HOH A 7 1107 1107 HOH HOH . F 4 HOH A 8 1108 1108 HOH HOH . F 4 HOH A 9 1109 1109 HOH HOH . F 4 HOH A 10 1110 1110 HOH HOH . F 4 HOH A 11 1111 1111 HOH HOH . F 4 HOH A 12 1112 1112 HOH HOH . F 4 HOH A 13 1113 1113 HOH HOH . F 4 HOH A 14 1114 1114 HOH HOH . F 4 HOH A 15 1115 1115 HOH HOH . F 4 HOH A 16 1116 1116 HOH HOH . F 4 HOH A 17 1117 1117 HOH HOH . F 4 HOH A 18 1118 1118 HOH HOH . F 4 HOH A 19 1119 1119 HOH HOH . F 4 HOH A 20 1120 1120 HOH HOH . F 4 HOH A 21 1121 1121 HOH HOH . F 4 HOH A 22 1122 1122 HOH HOH . F 4 HOH A 23 1123 1123 HOH HOH . F 4 HOH A 24 1124 1124 HOH HOH . F 4 HOH A 25 1125 1125 HOH HOH . F 4 HOH A 26 1126 1126 HOH HOH . F 4 HOH A 27 1127 1127 HOH HOH . F 4 HOH A 28 1128 1128 HOH HOH . F 4 HOH A 29 1129 1129 HOH HOH . F 4 HOH A 30 1130 1130 HOH HOH . F 4 HOH A 31 1131 1131 HOH HOH . F 4 HOH A 32 1132 1132 HOH HOH . F 4 HOH A 33 1133 1133 HOH HOH . F 4 HOH A 34 1134 1134 HOH HOH . F 4 HOH A 35 1135 1135 HOH HOH . F 4 HOH A 36 1136 1136 HOH HOH . F 4 HOH A 37 1137 1137 HOH HOH . F 4 HOH A 38 1138 1138 HOH HOH . F 4 HOH A 39 1139 1139 HOH HOH . F 4 HOH A 40 1140 1140 HOH HOH . F 4 HOH A 41 1141 1141 HOH HOH . F 4 HOH A 42 1142 1142 HOH HOH . F 4 HOH A 43 1143 1143 HOH HOH . F 4 HOH A 44 1144 1144 HOH HOH . F 4 HOH A 45 1145 1145 HOH HOH . F 4 HOH A 46 1146 1146 HOH HOH . F 4 HOH A 47 1147 1147 HOH HOH . F 4 HOH A 48 1148 1148 HOH HOH . F 4 HOH A 49 1149 1149 HOH HOH . F 4 HOH A 50 1150 1150 HOH HOH . F 4 HOH A 51 1151 1151 HOH HOH . F 4 HOH A 52 1152 1152 HOH HOH . F 4 HOH A 53 1153 1153 HOH HOH . F 4 HOH A 54 1154 1154 HOH HOH . F 4 HOH A 55 1155 1155 HOH HOH . F 4 HOH A 56 1156 1156 HOH HOH . F 4 HOH A 57 1157 1157 HOH HOH . F 4 HOH A 58 1158 1158 HOH HOH . F 4 HOH A 59 1159 1159 HOH HOH . F 4 HOH A 60 1160 1160 HOH HOH . F 4 HOH A 61 1161 1161 HOH HOH . F 4 HOH A 62 1162 1162 HOH HOH . F 4 HOH A 63 1163 1163 HOH HOH . F 4 HOH A 64 1164 1164 HOH HOH . F 4 HOH A 65 1165 1165 HOH HOH . F 4 HOH A 66 1166 1166 HOH HOH . F 4 HOH A 67 1167 1167 HOH HOH . F 4 HOH A 68 1168 1168 HOH HOH . F 4 HOH A 69 1169 1169 HOH HOH . F 4 HOH A 70 1170 1170 HOH HOH . F 4 HOH A 71 1171 1171 HOH HOH . F 4 HOH A 72 1172 1172 HOH HOH . F 4 HOH A 73 1173 1173 HOH HOH . F 4 HOH A 74 1174 1174 HOH HOH . F 4 HOH A 75 1175 1175 HOH HOH . F 4 HOH A 76 1176 1176 HOH HOH . F 4 HOH A 77 1177 1177 HOH HOH . F 4 HOH A 78 1178 1178 HOH HOH . F 4 HOH A 79 1179 1179 HOH HOH . F 4 HOH A 80 1180 1180 HOH HOH . F 4 HOH A 81 1181 1181 HOH HOH . F 4 HOH A 82 1182 1182 HOH HOH . F 4 HOH A 83 1183 1183 HOH HOH . F 4 HOH A 84 1184 1184 HOH HOH . F 4 HOH A 85 1185 1185 HOH HOH . F 4 HOH A 86 1186 1186 HOH HOH . F 4 HOH A 87 1187 1187 HOH HOH . F 4 HOH A 88 1188 1188 HOH HOH . F 4 HOH A 89 1189 1189 HOH HOH . F 4 HOH A 90 1190 1190 HOH HOH . F 4 HOH A 91 1191 1191 HOH HOH . F 4 HOH A 92 1192 1192 HOH HOH . F 4 HOH A 93 1193 1193 HOH HOH . F 4 HOH A 94 1194 1194 HOH HOH . F 4 HOH A 95 1195 1195 HOH HOH . F 4 HOH A 96 1196 1196 HOH HOH . F 4 HOH A 97 1197 1197 HOH HOH . F 4 HOH A 98 1198 1198 HOH HOH . F 4 HOH A 99 1199 1199 HOH HOH . F 4 HOH A 100 1200 1200 HOH HOH . F 4 HOH A 101 1201 1201 HOH HOH . F 4 HOH A 102 1202 1202 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 C C2 8LE . . . B 2 -13.618 -40.207 12.73 1 36.89 ? C2 8LE 1001 A 1 HETATM 2 C CAA 8LE . . . B 2 -20.747 -39.334 5.235 1 32.56 ? CAA 8LE 1001 A 1 HETATM 3 C CAZ 8LE . . . B 2 -19.66 -39.163 6.312 1 33.2 ? CAZ 8LE 1001 A 1 HETATM 4 C CAB 8LE . . . B 2 -19.567 -40.434 7.177 1 31.17 ? CAB 8LE 1001 A 1 HETATM 5 O OAF 8LE . . . B 2 -20.023 -38.09 7.17 1 30.69 ? OAF 8LE 1001 A 1 HETATM 6 C CAS 8LE . . . B 2 -18.301 -38.834 5.642 1 37.08 ? CAS 8LE 1001 A 1 HETATM 7 O OAD 8LE . . . B 2 -17.678 -37.82 5.948 1 38.09 ? OAD 8LE 1001 A 1 HETATM 8 O OAQ 8LE . . . B 2 -17.88 -39.72 4.692 1 39.96 ? OAQ 8LE 1001 A 1 HETATM 9 P PBC 8LE . . . B 2 -16.677 -39.481 3.596 1 38.94 ? PBC 8LE 1001 A 1 HETATM 10 O OAI 8LE . . . B 2 -16.857 -38.043 2.935 1 34.68 ? OAI 8LE 1001 A 1 HETATM 11 O OAE 8LE . . . B 2 -16.661 -40.594 2.619 1 44.06 ? OAE 8LE 1001 A 1 HETATM 12 O O5' 8LE . . . B 2 -15.336 -39.476 4.426 1 38.43 ? O5' 8LE 1001 A 1 HETATM 13 C C5' 8LE . . . B 2 -15.118 -40.613 5.251 1 35.22 ? C5' 8LE 1001 A 1 HETATM 14 C C4' 8LE . . . B 2 -13.883 -40.386 6.08 1 31.62 ? C4' 8LE 1001 A 1 HETATM 15 O O4' 8LE . . . B 2 -14.154 -39.315 7.018 1 31.34 ? O4' 8LE 1001 A 1 HETATM 16 C C3' 8LE . . . B 2 -13.703 -41.605 6.896 1 31.85 ? C3' 8LE 1001 A 1 HETATM 17 O O3' 8LE . . . B 2 -12.9 -42.541 6.169 1 30.83 ? O3' 8LE 1001 A 1 HETATM 18 C C2' 8LE . . . B 2 -12.983 -41.044 8.123 1 33.51 ? C2' 8LE 1001 A 1 HETATM 19 O O2' 8LE . . . B 2 -11.569 -40.778 7.879 1 35.26 ? O2' 8LE 1001 A 1 HETATM 20 C C1' 8LE . . . B 2 -13.704 -39.731 8.326 1 32.25 ? C1' 8LE 1001 A 1 HETATM 21 N N9 8LE . . . B 2 -14.842 -39.862 9.291 1 37.11 ? N9 8LE 1001 A 1 HETATM 22 C C8 8LE . . . B 2 -16.155 -39.876 9.035 1 37.48 ? C8 8LE 1001 A 1 HETATM 23 N N7 8LE . . . B 2 -16.799 -40.012 10.189 1 38.24 ? N7 8LE 1001 A 1 HETATM 24 C C5 8LE . . . B 2 -15.892 -40.101 11.168 1 38.48 ? C5 8LE 1001 A 1 HETATM 25 C C4 8LE . . . B 2 -14.674 -40.01 10.603 1 38.12 ? C4 8LE 1001 A 1 HETATM 26 N N3 8LE . . . B 2 -13.544 -40.041 11.348 1 36.73 ? N3 8LE 1001 A 1 HETATM 27 N N1 8LE . . . B 2 -14.895 -40.299 13.29 1 38.11 ? N1 8LE 1001 A 1 HETATM 28 C C6 8LE . . . B 2 -15.987 -40.224 12.506 1 37.59 ? C6 8LE 1001 A 1 HETATM 29 N N6 8LE . . . B 2 -17.198 -40.294 13.044 1 35.34 ? N6 8LE 1001 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 29 #