data_3DGA # _model_server_result.job_id jjLsmyOqBltpjedcEo-oyw _model_server_result.datetime_utc '2024-11-23 07:24:17' _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 3dga # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":611}' # _entry.id 3DGA # _exptl.entry_id 3DGA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 3DGA _cell.length_a 57.377 _cell.length_b 156.015 _cell.length_c 164.567 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DGA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,I,K,M 1 1 B,D,G,H,J,L,N 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 I N N ? 5 J N N # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 N1 C2 UMP sing 467 n n N1 C6 UMP sing 468 n n N1 C1' UMP sing 469 n n C2 N3 UMP sing 470 n n C2 O2 UMP doub 471 n n N3 C4 UMP sing 472 n n N3 HN3 UMP sing 473 n n C4 C5 UMP sing 474 n n C4 O4 UMP doub 475 n n C5 C6 UMP doub 476 n n C5 H5 UMP sing 477 n n C6 H6 UMP sing 478 n n C1' C2' UMP sing 479 n n C1' O4' UMP sing 480 n n C1' H1' UMP sing 481 n n C2' C3' UMP sing 482 n n C2' H2' UMP sing 483 n n C2' "H2''" UMP sing 484 n n C3' C4' UMP sing 485 n n C3' O3' UMP sing 486 n n C3' H3' UMP sing 487 n n C4' O4' UMP sing 488 n n C4' C5' UMP sing 489 n n C4' H4' UMP sing 490 n n O3' HO3' UMP sing 491 n n C5' O5' UMP sing 492 n n C5' H5' UMP sing 493 n n C5' "H5''" UMP sing 494 n n O5' P UMP sing 495 n n P OP1 UMP doub 496 n n P OP2 UMP sing 497 n n P OP3 UMP sing 498 n n OP2 HOP2 UMP sing 499 n n OP3 HOP3 UMP sing 500 n n # _atom_sites.entry_id 3DGA _atom_sites.fract_transf_matrix[1][1] 0.017429 _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] 0.00641 _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] 0.006077 _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 E 3 RJ1 A 1 609 609 RJ1 RJ1 . F 4 NDP A 1 610 610 NDP NDP . G 3 RJ1 B 1 609 609 RJ1 RJ1 . H 4 NDP B 1 610 610 NDP NDP . I 5 UMP C 1 611 611 UMP UMP . J 5 UMP D 1 611 611 UMP UMP . K 6 HOH A 1 1020 1020 HOH HOH . K 6 HOH A 2 1029 1029 HOH HOH . K 6 HOH A 3 1030 1030 HOH HOH . K 6 HOH A 4 1033 1033 HOH HOH . K 6 HOH A 5 1047 1047 HOH HOH . K 6 HOH A 6 1056 1056 HOH HOH . K 6 HOH A 7 1059 1059 HOH HOH . K 6 HOH A 8 1063 1063 HOH HOH . K 6 HOH A 9 1064 1064 HOH HOH . K 6 HOH A 10 1065 1065 HOH HOH . K 6 HOH A 11 1066 1066 HOH HOH . K 6 HOH A 12 1073 1073 HOH HOH . K 6 HOH A 13 1093 1093 HOH HOH . K 6 HOH A 14 1105 1105 HOH HOH . K 6 HOH A 15 1109 1109 HOH HOH . K 6 HOH A 16 1124 1124 HOH HOH . K 6 HOH A 17 1131 1131 HOH HOH . K 6 HOH A 18 1133 1133 HOH HOH . K 6 HOH A 19 1138 1138 HOH HOH . K 6 HOH A 20 1146 1146 HOH HOH . K 6 HOH A 21 1154 1154 HOH HOH . K 6 HOH A 22 1156 1156 HOH HOH . K 6 HOH A 23 1159 1159 HOH HOH . K 6 HOH A 24 1172 1172 HOH HOH . K 6 HOH A 25 1175 1175 HOH HOH . K 6 HOH A 26 1177 1177 HOH HOH . K 6 HOH A 27 1182 1182 HOH HOH . K 6 HOH A 28 1187 1187 HOH HOH . K 6 HOH A 29 1193 1193 HOH HOH . K 6 HOH A 30 1195 1195 HOH HOH . K 6 HOH A 31 1198 1198 HOH HOH . K 6 HOH A 32 1203 1203 HOH HOH . K 6 HOH A 33 1204 1204 HOH HOH . K 6 HOH A 34 1215 1215 HOH HOH . K 6 HOH A 35 1218 1218 HOH HOH . K 6 HOH A 36 1220 1220 HOH HOH . K 6 HOH A 37 1224 1224 HOH HOH . K 6 HOH A 38 1225 1225 HOH HOH . K 6 HOH A 39 1232 1232 HOH HOH . K 6 HOH A 40 1234 1234 HOH HOH . K 6 HOH A 41 1236 1236 HOH HOH . K 6 HOH A 42 1238 1238 HOH HOH . K 6 HOH A 43 1240 1240 HOH HOH . K 6 HOH A 44 1244 1244 HOH HOH . L 6 HOH B 1 1017 1017 HOH HOH . L 6 HOH B 2 1055 1055 HOH HOH . L 6 HOH B 3 1072 1072 HOH HOH . L 6 HOH B 4 1091 1091 HOH HOH . L 6 HOH B 5 1110 1110 HOH HOH . L 6 HOH B 6 1136 1136 HOH HOH . L 6 HOH B 7 1137 1137 HOH HOH . L 6 HOH B 8 1142 1142 HOH HOH . L 6 HOH B 9 1157 1157 HOH HOH . L 6 HOH B 10 1158 1158 HOH HOH . L 6 HOH B 11 1166 1166 HOH HOH . L 6 HOH B 12 1183 1183 HOH HOH . L 6 HOH B 13 1200 1200 HOH HOH . L 6 HOH B 14 1219 1219 HOH HOH . L 6 HOH B 15 1227 1227 HOH HOH . L 6 HOH B 16 1228 1228 HOH HOH . L 6 HOH B 17 1230 1230 HOH HOH . L 6 HOH B 18 1235 1235 HOH HOH . M 6 HOH C 1 1001 1001 HOH HOH . M 6 HOH C 2 1002 1002 HOH HOH . M 6 HOH C 3 1007 1007 HOH HOH . M 6 HOH C 4 1010 1010 HOH HOH . M 6 HOH C 5 1011 1011 HOH HOH . M 6 HOH C 6 1014 1014 HOH HOH . M 6 HOH C 7 1016 1016 HOH HOH . M 6 HOH C 8 1021 1021 HOH HOH . M 6 HOH C 9 1024 1024 HOH HOH . M 6 HOH C 10 1026 1026 HOH HOH . M 6 HOH C 11 1027 1027 HOH HOH . M 6 HOH C 12 1035 1035 HOH HOH . M 6 HOH C 13 1037 1037 HOH HOH . M 6 HOH C 14 1038 1038 HOH HOH . M 6 HOH C 15 1039 1039 HOH HOH . M 6 HOH C 16 1042 1042 HOH HOH . M 6 HOH C 17 1046 1046 HOH HOH . M 6 HOH C 18 1049 1049 HOH HOH . M 6 HOH C 19 1052 1052 HOH HOH . M 6 HOH C 20 1053 1053 HOH HOH . M 6 HOH C 21 1057 1057 HOH HOH . M 6 HOH C 22 1058 1058 HOH HOH . M 6 HOH C 23 1061 1061 HOH HOH . M 6 HOH C 24 1062 1062 HOH HOH . M 6 HOH C 25 1067 1067 HOH HOH . M 6 HOH C 26 1068 1068 HOH HOH . M 6 HOH C 27 1070 1070 HOH HOH . M 6 HOH C 28 1074 1074 HOH HOH . M 6 HOH C 29 1075 1075 HOH HOH . M 6 HOH C 30 1077 1077 HOH HOH . M 6 HOH C 31 1082 1082 HOH HOH . M 6 HOH C 32 1083 1083 HOH HOH . M 6 HOH C 33 1085 1085 HOH HOH . M 6 HOH C 34 1087 1087 HOH HOH . M 6 HOH C 35 1095 1095 HOH HOH . M 6 HOH C 36 1096 1096 HOH HOH . M 6 HOH C 37 1098 1098 HOH HOH . M 6 HOH C 38 1106 1106 HOH HOH . M 6 HOH C 39 1112 1112 HOH HOH . M 6 HOH C 40 1113 1113 HOH HOH . M 6 HOH C 41 1114 1114 HOH HOH . M 6 HOH C 42 1117 1117 HOH HOH . M 6 HOH C 43 1118 1118 HOH HOH . M 6 HOH C 44 1121 1121 HOH HOH . M 6 HOH C 45 1123 1123 HOH HOH . M 6 HOH C 46 1125 1125 HOH HOH . M 6 HOH C 47 1126 1126 HOH HOH . M 6 HOH C 48 1127 1127 HOH HOH . M 6 HOH C 49 1134 1134 HOH HOH . M 6 HOH C 50 1139 1139 HOH HOH . M 6 HOH C 51 1141 1141 HOH HOH . M 6 HOH C 52 1143 1143 HOH HOH . M 6 HOH C 53 1145 1145 HOH HOH . M 6 HOH C 54 1148 1148 HOH HOH . M 6 HOH C 55 1149 1149 HOH HOH . M 6 HOH C 56 1150 1150 HOH HOH . M 6 HOH C 57 1153 1153 HOH HOH . M 6 HOH C 58 1160 1160 HOH HOH . M 6 HOH C 59 1162 1162 HOH HOH . M 6 HOH C 60 1163 1163 HOH HOH . M 6 HOH C 61 1164 1164 HOH HOH . M 6 HOH C 62 1167 1167 HOH HOH . M 6 HOH C 63 1171 1171 HOH HOH . M 6 HOH C 64 1173 1173 HOH HOH . M 6 HOH C 65 1174 1174 HOH HOH . M 6 HOH C 66 1176 1176 HOH HOH . M 6 HOH C 67 1179 1179 HOH HOH . M 6 HOH C 68 1180 1180 HOH HOH . M 6 HOH C 69 1181 1181 HOH HOH . M 6 HOH C 70 1184 1184 HOH HOH . M 6 HOH C 71 1186 1186 HOH HOH . M 6 HOH C 72 1188 1188 HOH HOH . M 6 HOH C 73 1194 1194 HOH HOH . M 6 HOH C 74 1197 1197 HOH HOH . M 6 HOH C 75 1205 1205 HOH HOH . M 6 HOH C 76 1209 1209 HOH HOH . M 6 HOH C 77 1210 1210 HOH HOH . M 6 HOH C 78 1216 1216 HOH HOH . M 6 HOH C 79 1221 1221 HOH HOH . M 6 HOH C 80 1222 1222 HOH HOH . M 6 HOH C 81 1223 1223 HOH HOH . M 6 HOH C 82 1226 1226 HOH HOH . M 6 HOH C 83 1231 1231 HOH HOH . M 6 HOH C 84 1237 1237 HOH HOH . M 6 HOH C 85 1239 1239 HOH HOH . M 6 HOH C 86 1243 1243 HOH HOH . M 6 HOH C 87 1245 1245 HOH HOH . M 6 HOH C 88 1249 1249 HOH HOH . N 6 HOH D 1 1003 1003 HOH HOH . N 6 HOH D 2 1004 1004 HOH HOH . N 6 HOH D 3 1005 1005 HOH HOH . N 6 HOH D 4 1006 1006 HOH HOH . N 6 HOH D 5 1008 1008 HOH HOH . N 6 HOH D 6 1009 1009 HOH HOH . N 6 HOH D 7 1012 1012 HOH HOH . N 6 HOH D 8 1013 1013 HOH HOH . N 6 HOH D 9 1015 1015 HOH HOH . N 6 HOH D 10 1018 1018 HOH HOH . N 6 HOH D 11 1019 1019 HOH HOH . N 6 HOH D 12 1022 1022 HOH HOH . N 6 HOH D 13 1023 1023 HOH HOH . N 6 HOH D 14 1025 1025 HOH HOH . N 6 HOH D 15 1028 1028 HOH HOH . N 6 HOH D 16 1031 1031 HOH HOH . N 6 HOH D 17 1032 1032 HOH HOH . N 6 HOH D 18 1034 1034 HOH HOH . N 6 HOH D 19 1036 1036 HOH HOH . N 6 HOH D 20 1040 1040 HOH HOH . N 6 HOH D 21 1041 1041 HOH HOH . N 6 HOH D 22 1043 1043 HOH HOH . N 6 HOH D 23 1044 1044 HOH HOH . N 6 HOH D 24 1045 1045 HOH HOH . N 6 HOH D 25 1048 1048 HOH HOH . N 6 HOH D 26 1050 1050 HOH HOH . N 6 HOH D 27 1051 1051 HOH HOH . N 6 HOH D 28 1054 1054 HOH HOH . N 6 HOH D 29 1060 1060 HOH HOH . N 6 HOH D 30 1069 1069 HOH HOH . N 6 HOH D 31 1071 1071 HOH HOH . N 6 HOH D 32 1076 1076 HOH HOH . N 6 HOH D 33 1078 1078 HOH HOH . N 6 HOH D 34 1079 1079 HOH HOH . N 6 HOH D 35 1080 1080 HOH HOH . N 6 HOH D 36 1081 1081 HOH HOH . N 6 HOH D 37 1084 1084 HOH HOH . N 6 HOH D 38 1086 1086 HOH HOH . N 6 HOH D 39 1088 1088 HOH HOH . N 6 HOH D 40 1089 1089 HOH HOH . N 6 HOH D 41 1090 1090 HOH HOH . N 6 HOH D 42 1092 1092 HOH HOH . N 6 HOH D 43 1094 1094 HOH HOH . N 6 HOH D 44 1097 1097 HOH HOH . N 6 HOH D 45 1099 1099 HOH HOH . N 6 HOH D 46 1100 1100 HOH HOH . N 6 HOH D 47 1101 1101 HOH HOH . N 6 HOH D 48 1102 1102 HOH HOH . N 6 HOH D 49 1103 1103 HOH HOH . N 6 HOH D 50 1104 1104 HOH HOH . N 6 HOH D 51 1107 1107 HOH HOH . N 6 HOH D 52 1108 1108 HOH HOH . N 6 HOH D 53 1111 1111 HOH HOH . N 6 HOH D 54 1115 1115 HOH HOH . N 6 HOH D 55 1116 1116 HOH HOH . N 6 HOH D 56 1119 1119 HOH HOH . N 6 HOH D 57 1120 1120 HOH HOH . N 6 HOH D 58 1122 1122 HOH HOH . N 6 HOH D 59 1128 1128 HOH HOH . N 6 HOH D 60 1129 1129 HOH HOH . N 6 HOH D 61 1130 1130 HOH HOH . N 6 HOH D 62 1132 1132 HOH HOH . N 6 HOH D 63 1135 1135 HOH HOH . N 6 HOH D 64 1140 1140 HOH HOH . N 6 HOH D 65 1144 1144 HOH HOH . N 6 HOH D 66 1147 1147 HOH HOH . N 6 HOH D 67 1151 1151 HOH HOH . N 6 HOH D 68 1152 1152 HOH HOH . N 6 HOH D 69 1155 1155 HOH HOH . N 6 HOH D 70 1161 1161 HOH HOH . N 6 HOH D 71 1165 1165 HOH HOH . N 6 HOH D 72 1168 1168 HOH HOH . N 6 HOH D 73 1169 1169 HOH HOH . N 6 HOH D 74 1170 1170 HOH HOH . N 6 HOH D 75 1178 1178 HOH HOH . N 6 HOH D 76 1185 1185 HOH HOH . N 6 HOH D 77 1189 1189 HOH HOH . N 6 HOH D 78 1190 1190 HOH HOH . N 6 HOH D 79 1191 1191 HOH HOH . N 6 HOH D 80 1192 1192 HOH HOH . N 6 HOH D 81 1196 1196 HOH HOH . N 6 HOH D 82 1199 1199 HOH HOH . N 6 HOH D 83 1201 1201 HOH HOH . N 6 HOH D 84 1202 1202 HOH HOH . N 6 HOH D 85 1206 1206 HOH HOH . N 6 HOH D 86 1207 1207 HOH HOH . N 6 HOH D 87 1208 1208 HOH HOH . N 6 HOH D 88 1211 1211 HOH HOH . N 6 HOH D 89 1212 1212 HOH HOH . N 6 HOH D 90 1213 1213 HOH HOH . N 6 HOH D 91 1214 1214 HOH HOH . N 6 HOH D 92 1217 1217 HOH HOH . N 6 HOH D 93 1229 1229 HOH HOH . N 6 HOH D 94 1233 1233 HOH HOH . N 6 HOH D 95 1241 1241 HOH HOH . N 6 HOH D 96 1242 1242 HOH HOH . N 6 HOH D 97 1246 1246 HOH HOH . N 6 HOH D 98 1247 1247 HOH HOH . N 6 HOH D 99 1248 1248 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 N N1 UMP . . . I 5 44.236 20.332 19.379 1 49.05 ? N1 UMP 611 C 1 HETATM 2 C C2 UMP . . . I 5 43.447 19.735 20.403 1 48.87 ? C2 UMP 611 C 1 HETATM 3 N N3 UMP . . . I 5 42.549 20.625 21.02 1 50.99 ? N3 UMP 611 C 1 HETATM 4 C C4 UMP . . . I 5 42.382 22.007 20.707 1 52.36 ? C4 UMP 611 C 1 HETATM 5 C C5 UMP . . . I 5 43.238 22.522 19.641 1 51.46 ? C5 UMP 611 C 1 HETATM 6 C C6 UMP . . . I 5 44.135 21.64 19.024 1 50 ? C6 UMP 611 C 1 HETATM 7 O O2 UMP . . . I 5 43.509 18.564 20.748 1 45.78 ? O2 UMP 611 C 1 HETATM 8 O O4 UMP . . . I 5 41.578 22.726 21.289 1 53.38 ? O4 UMP 611 C 1 HETATM 9 C C1' UMP . . . I 5 45.262 19.565 18.586 1 48.65 ? C1' UMP 611 C 1 HETATM 10 C C2' UMP . . . I 5 44.817 18.467 17.595 1 46.94 ? C2' UMP 611 C 1 HETATM 11 C C3' UMP . . . I 5 46.012 18.298 16.653 1 46.22 ? C3' UMP 611 C 1 HETATM 12 C C4' UMP . . . I 5 46.642 19.699 16.455 1 46.67 ? C4' UMP 611 C 1 HETATM 13 O O3' UMP . . . I 5 46.965 17.444 17.339 1 42.84 ? O3' UMP 611 C 1 HETATM 14 O O4' UMP . . . I 5 46.175 20.382 17.696 1 47.21 ? O4' UMP 611 C 1 HETATM 15 C C5' UMP . . . I 5 46.038 20.432 15.26 1 44.64 ? C5' UMP 611 C 1 HETATM 16 O O5' UMP . . . I 5 46.451 19.754 14.04 1 43.28 ? O5' UMP 611 C 1 HETATM 17 P P UMP . . . I 5 45.549 19.662 12.772 1 43.86 ? P UMP 611 C 1 HETATM 18 O OP1 UMP . . . I 5 44.367 18.835 13.005 1 42.77 ? OP1 UMP 611 C 1 HETATM 19 O OP2 UMP . . . I 5 45.17 21.047 12.461 1 40.3 ? OP2 UMP 611 C 1 HETATM 20 O OP3 UMP . . . I 5 46.308 19.067 11.68 1 43.58 ? OP3 UMP 611 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 20 #