data_1G3U # _model_server_result.job_id 7IyeRqtaW59bcft_hKaCrQ _model_server_result.datetime_utc '2024-10-26 18:23:45' _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 1g3u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":217}' # _entry.id 1G3U # _exptl.entry_id 1G3U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-PHOSPHATE" _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 120 _cell.entry_id 1G3U _cell.length_a 76.622 _cell.length_b 76.622 _cell.length_c 134.378 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1G3U _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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' 8_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 9 A ASP 9 1_555 D MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc2 A OE2 GLU 166 A GLU 166 1_555 D MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc3 E O2P TMP . A TMP 217 1_555 D MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc4 D MG MG . A MG 300 1_555 F O HOH . A HOH 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc5 D MG MG . A MG 300 1_555 F O HOH . A HOH 1018 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc6 D MG MG . A MG 300 1_555 F O HOH . A HOH 1050 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? # _chem_comp.formula 'C10 H15 N2 O8 P' _chem_comp.formula_weight 322.208 _chem_comp.id TMP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-PHOSPHATE" _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 P O1P TMP doub 310 n n P O2P TMP sing 311 n n P O3P TMP sing 312 n n P O5' TMP sing 313 n n O2P HOP2 TMP sing 314 n n O3P HOP3 TMP sing 315 n n O5' C5' TMP sing 316 n n C5' C4' TMP sing 317 n n C5' "H5'1" TMP sing 318 n n C5' "H5'2" TMP sing 319 n n C4' O4' TMP sing 320 n n C4' C3' TMP sing 321 n n C4' H4' TMP sing 322 n n O4' C1' TMP sing 323 n n C3' O3' TMP sing 324 n n C3' C2' TMP sing 325 n n C3' H3' TMP sing 326 n n O3' HO3' TMP sing 327 n n C2' C1' TMP sing 328 n n C2' "H2'1" TMP sing 329 n n C2' "H2'2" TMP sing 330 n n C1' N1 TMP sing 331 n n C1' H1' TMP sing 332 n n N1 C2 TMP sing 333 n n N1 C6 TMP sing 334 n n C2 O2 TMP doub 335 n n C2 N3 TMP sing 336 n n N3 C4 TMP sing 337 n n N3 HN3 TMP sing 338 n n C4 O4 TMP doub 339 n n C4 C5 TMP sing 340 n n C5 C5M TMP sing 341 n n C5 C6 TMP doub 342 n n C5M H51 TMP sing 343 n n C5M H52 TMP sing 344 n n C5M H53 TMP sing 345 n n C6 H6 TMP sing 346 n n # _atom_sites.entry_id 1G3U _atom_sites.fract_transf_matrix[1][1] 0.013051 _atom_sites.fract_transf_matrix[1][2] 0.007535 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01507 _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] 0.007442 _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 SO4 A 1 219 219 SO4 SUL . C 2 SO4 A 1 220 220 SO4 SUL . D 3 MG A 1 300 300 MG MG . E 4 TMP A 1 217 217 TMP TMP . F 5 HOH A 1 1001 1001 HOH HOH . F 5 HOH A 2 1002 1002 HOH HOH . F 5 HOH A 3 1003 1003 HOH HOH . F 5 HOH A 4 1004 1004 HOH HOH . F 5 HOH A 5 1005 1005 HOH HOH . F 5 HOH A 6 1006 1006 HOH HOH . F 5 HOH A 7 1007 1007 HOH HOH . F 5 HOH A 8 1008 1008 HOH HOH . F 5 HOH A 9 1009 1009 HOH HOH . F 5 HOH A 10 1010 1010 HOH HOH . F 5 HOH A 11 1011 1011 HOH HOH . F 5 HOH A 12 1012 1012 HOH HOH . F 5 HOH A 13 1013 1013 HOH HOH . F 5 HOH A 14 1014 1014 HOH HOH . F 5 HOH A 15 1015 1015 HOH HOH . F 5 HOH A 16 1016 1016 HOH HOH . F 5 HOH A 17 1017 1017 HOH HOH . F 5 HOH A 18 1018 1018 HOH HOH . F 5 HOH A 19 1019 1019 HOH HOH . F 5 HOH A 20 1020 1020 HOH HOH . F 5 HOH A 21 1021 1021 HOH HOH . F 5 HOH A 22 1022 1022 HOH HOH . F 5 HOH A 23 1023 1023 HOH HOH . F 5 HOH A 24 1024 1024 HOH HOH . F 5 HOH A 25 1025 1025 HOH HOH . F 5 HOH A 26 1026 1026 HOH HOH . F 5 HOH A 27 1027 1027 HOH HOH . F 5 HOH A 28 1028 1028 HOH HOH . F 5 HOH A 29 1029 1029 HOH HOH . F 5 HOH A 30 1030 1030 HOH HOH . F 5 HOH A 31 1031 1031 HOH HOH . F 5 HOH A 32 1032 1032 HOH HOH . F 5 HOH A 33 1033 1033 HOH HOH . F 5 HOH A 34 1034 1034 HOH HOH . F 5 HOH A 35 1035 1035 HOH HOH . F 5 HOH A 36 1036 1036 HOH HOH . F 5 HOH A 37 1037 1037 HOH HOH . F 5 HOH A 38 1038 1038 HOH HOH . F 5 HOH A 39 1039 1039 HOH HOH . F 5 HOH A 40 1040 1040 HOH HOH . F 5 HOH A 41 1041 1041 HOH HOH . F 5 HOH A 42 1042 1042 HOH HOH . F 5 HOH A 43 1043 1043 HOH HOH . F 5 HOH A 44 1044 1044 HOH HOH . F 5 HOH A 45 1045 1045 HOH HOH . F 5 HOH A 46 1046 1046 HOH HOH . F 5 HOH A 47 1047 1047 HOH HOH . F 5 HOH A 48 1048 1048 HOH HOH . F 5 HOH A 49 1049 1049 HOH HOH . F 5 HOH A 50 1050 1050 HOH HOH . F 5 HOH A 51 1051 1051 HOH HOH . F 5 HOH A 52 1052 1052 HOH HOH . F 5 HOH A 53 1053 1053 HOH HOH . F 5 HOH A 54 1054 1054 HOH HOH . F 5 HOH A 55 1055 1055 HOH HOH . F 5 HOH A 56 1056 1056 HOH HOH . F 5 HOH A 57 1057 1057 HOH HOH . F 5 HOH A 58 1058 1058 HOH HOH . F 5 HOH A 59 1059 1059 HOH HOH . F 5 HOH A 60 1060 1060 HOH HOH . F 5 HOH A 61 1061 1061 HOH HOH . F 5 HOH A 62 1062 1062 HOH HOH . F 5 HOH A 63 1063 1063 HOH HOH . F 5 HOH A 64 1064 1064 HOH HOH . F 5 HOH A 65 1065 1065 HOH HOH . F 5 HOH A 66 1066 1066 HOH HOH . F 5 HOH A 67 1067 1067 HOH HOH . F 5 HOH A 68 1068 1068 HOH HOH . F 5 HOH A 69 1069 1069 HOH HOH . F 5 HOH A 70 1070 1070 HOH HOH . F 5 HOH A 71 1071 1071 HOH HOH . F 5 HOH A 72 1072 1072 HOH HOH . F 5 HOH A 73 1073 1073 HOH HOH . F 5 HOH A 74 1074 1074 HOH HOH . F 5 HOH A 75 1075 1075 HOH HOH . F 5 HOH A 76 1076 1076 HOH HOH . F 5 HOH A 77 1077 1077 HOH HOH . F 5 HOH A 78 1078 1078 HOH HOH . F 5 HOH A 79 1079 1079 HOH HOH . F 5 HOH A 80 1080 1080 HOH HOH . F 5 HOH A 81 1081 1081 HOH HOH . F 5 HOH A 82 1082 1082 HOH HOH . F 5 HOH A 83 1083 1083 HOH HOH . F 5 HOH A 84 1084 1084 HOH HOH . F 5 HOH A 85 1085 1085 HOH HOH . F 5 HOH A 86 1086 1086 HOH HOH . F 5 HOH A 87 1087 1087 HOH HOH . F 5 HOH A 88 1088 1088 HOH HOH . F 5 HOH A 89 1089 1089 HOH HOH . F 5 HOH A 90 1090 1090 HOH HOH . F 5 HOH A 91 1091 1091 HOH HOH . F 5 HOH A 92 1092 1092 HOH HOH . F 5 HOH A 93 1093 1093 HOH HOH . F 5 HOH A 94 1094 1094 HOH HOH . F 5 HOH A 95 1095 1095 HOH HOH . F 5 HOH A 96 1096 1096 HOH HOH . F 5 HOH A 97 1097 1097 HOH HOH . F 5 HOH A 98 1098 1098 HOH HOH . F 5 HOH A 99 1099 1099 HOH HOH . F 5 HOH A 100 1100 1100 HOH HOH . F 5 HOH A 101 1101 1101 HOH HOH . F 5 HOH A 102 1102 1102 HOH HOH . F 5 HOH A 103 1103 1103 HOH HOH . F 5 HOH A 104 1104 1104 HOH HOH . F 5 HOH A 105 1105 1105 HOH HOH . F 5 HOH A 106 1106 1106 HOH HOH . F 5 HOH A 107 1107 1107 HOH HOH . F 5 HOH A 108 1108 1108 HOH HOH . F 5 HOH A 109 1109 1109 HOH HOH . F 5 HOH A 110 1110 1110 HOH HOH . F 5 HOH A 111 1111 1111 HOH HOH . F 5 HOH A 112 1112 1112 HOH HOH . F 5 HOH A 113 1113 1113 HOH HOH . F 5 HOH A 114 1114 1114 HOH HOH . F 5 HOH A 115 1115 1115 HOH HOH . F 5 HOH A 116 1116 1116 HOH HOH . F 5 HOH A 117 1117 1117 HOH HOH . F 5 HOH A 118 1118 1118 HOH HOH . F 5 HOH A 119 1119 1119 HOH HOH . F 5 HOH A 120 1120 1120 HOH HOH . F 5 HOH A 121 1121 1121 HOH HOH . F 5 HOH A 122 1122 1122 HOH HOH . F 5 HOH A 123 1123 1123 HOH HOH . F 5 HOH A 124 1124 1124 HOH HOH . F 5 HOH A 125 1125 1125 HOH HOH . F 5 HOH A 126 1126 1126 HOH HOH . F 5 HOH A 127 1127 1127 HOH HOH . F 5 HOH A 128 1128 1128 HOH HOH . F 5 HOH A 129 1129 1129 HOH HOH . F 5 HOH A 130 1130 1130 HOH HOH . F 5 HOH A 131 1131 1131 HOH HOH . F 5 HOH A 132 1132 1132 HOH HOH . F 5 HOH A 133 1133 1133 HOH HOH . F 5 HOH A 134 1134 1134 HOH HOH . F 5 HOH A 135 1135 1135 HOH HOH . F 5 HOH A 136 1136 1136 HOH HOH . F 5 HOH A 137 1137 1137 HOH HOH . F 5 HOH A 138 1138 1138 HOH HOH . F 5 HOH A 139 1139 1139 HOH HOH . F 5 HOH A 140 1140 1140 HOH HOH . F 5 HOH A 141 1141 1141 HOH HOH . F 5 HOH A 142 1142 1142 HOH HOH . F 5 HOH A 143 1143 1143 HOH HOH . F 5 HOH A 144 1144 1144 HOH HOH . F 5 HOH A 145 1145 1145 HOH HOH . F 5 HOH A 146 1146 1146 HOH HOH . F 5 HOH A 147 1147 1147 HOH HOH . F 5 HOH A 148 1148 1148 HOH HOH . F 5 HOH A 149 1149 1149 HOH HOH . F 5 HOH A 150 1150 1150 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 P P TMP . . . E 4 26.346 14.858 8.421 1 33.12 ? P TMP 217 A 1 HETATM 2 O O1P TMP . . . E 4 27.493 14.761 9.42 1 31.33 ? O1P TMP 217 A 1 HETATM 3 O O2P TMP . . . E 4 25.214 15.508 9.133 1 32.58 ? O2P TMP 217 A 1 HETATM 4 O O3P TMP . . . E 4 27.188 15.702 7.672 1 31.33 ? O3P TMP 217 A 1 HETATM 5 O O5' TMP . . . E 4 25.912 13.32 8.095 1 27.37 ? O5' TMP 217 A 1 HETATM 6 C C5' TMP . . . E 4 24.978 13.09 7.028 1 24.94 ? C5' TMP 217 A 1 HETATM 7 C C4' TMP . . . E 4 23.755 12.551 7.613 1 22.21 ? C4' TMP 217 A 1 HETATM 8 O O4' TMP . . . E 4 23.806 11.097 7.678 1 19.29 ? O4' TMP 217 A 1 HETATM 9 C C3' TMP . . . E 4 23.193 13.049 8.965 1 21 ? C3' TMP 217 A 1 HETATM 10 O O3' TMP . . . E 4 21.778 13.302 8.872 1 19.43 ? O3' TMP 217 A 1 HETATM 11 C C2' TMP . . . E 4 23.461 11.916 9.943 1 20.54 ? C2' TMP 217 A 1 HETATM 12 C C1' TMP . . . E 4 23.595 10.668 9.012 1 20.32 ? C1' TMP 217 A 1 HETATM 13 N N1 TMP . . . E 4 24.452 9.521 9.4 1 17.83 ? N1 TMP 217 A 1 HETATM 14 C C2 TMP . . . E 4 23.964 8.235 9.614 1 17.41 ? C2 TMP 217 A 1 HETATM 15 O O2 TMP . . . E 4 22.787 7.911 9.516 1 18.03 ? O2 TMP 217 A 1 HETATM 16 N N3 TMP . . . E 4 24.989 7.335 9.967 1 16.95 ? N3 TMP 217 A 1 HETATM 17 C C4 TMP . . . E 4 26.338 7.632 10.098 1 15.85 ? C4 TMP 217 A 1 HETATM 18 O O4 TMP . . . E 4 27.169 6.778 10.408 1 15.62 ? O4 TMP 217 A 1 HETATM 19 C C5 TMP . . . E 4 26.754 9.035 9.838 1 17.08 ? C5 TMP 217 A 1 HETATM 20 C C5M TMP . . . E 4 28.185 9.391 9.964 1 18.04 ? C5M TMP 217 A 1 HETATM 21 C C6 TMP . . . E 4 25.762 9.921 9.495 1 17.77 ? C6 TMP 217 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #