data_1N5J # _model_server_result.job_id '_QbnzHnujP6Vfr1wMoRiaQ' _model_server_result.datetime_utc '2024-11-24 23:15:07' _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 1n5j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":218}' # _entry.id 1N5J # _exptl.entry_id 1N5J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-DIPHOSPHATE" _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 1N5J _cell.length_a 76.248 _cell.length_b 76.248 _cell.length_c 135.114 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1N5J _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,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_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 217 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.399 ? metalc ? metalc2 A OD1 ASP 9 A ASP 9 1_555 D MG MG . A MG 217 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.158 ? metalc ? metalc3 A OE1 GLU 166 A GLU 166 1_555 D MG MG . A MG 217 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.217 ? metalc ? metalc4 A OE1 GLU 166 A GLU 166 1_555 D MG MG . A MG 217 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.267 ? metalc ? metalc5 D MG MG . A MG 217 1_555 E O2A TYD . A TYD 218 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.087 ? metalc ? metalc6 D MG MG . A MG 217 1_555 E O2B TYD . A TYD 218 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.958 ? metalc ? metalc7 D MG MG . A MG 217 1_555 F O2A TTP . A TTP 219 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.433 ? metalc ? metalc8 D MG MG . A MG 217 1_555 F O2B TTP . A TTP 219 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.394 ? metalc ? metalc9 D MG MG . A MG 217 1_555 G O HOH . A HOH 1009 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.952 ? metalc ? metalc10 D MG MG . A MG 217 1_555 G O HOH . A HOH 1009 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.547 ? metalc ? metalc11 D MG MG . A MG 217 1_555 G O HOH . A HOH 1018 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.156 ? metalc ? metalc12 D MG MG . A MG 217 1_555 G O HOH . A HOH 1018 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.563 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _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 PA O1A TYD doub 385 n n PA O2A TYD sing 386 n n PA O3A TYD sing 387 n n PA O5' TYD sing 388 n n O2A HOA2 TYD sing 389 n n O3A PB TYD sing 390 n n PB O1B TYD doub 391 n n PB O2B TYD sing 392 n n PB O3B TYD sing 393 n n O2B HOB2 TYD sing 394 n n O3B HOB3 TYD sing 395 n n O5' C5' TYD sing 396 n n C5' C4' TYD sing 397 n n C5' "H5'1" TYD sing 398 n n C5' "H5'2" TYD sing 399 n n C4' O4' TYD sing 400 n n C4' C3' TYD sing 401 n n C4' H4' TYD sing 402 n n O4' C1' TYD sing 403 n n C3' O3' TYD sing 404 n n C3' C2' TYD sing 405 n n C3' H3' TYD sing 406 n n O3' HO3' TYD sing 407 n n C2' C1' TYD sing 408 n n C2' "H2'1" TYD sing 409 n n C2' "H2'2" TYD sing 410 n n C1' N1 TYD sing 411 n n C1' H1' TYD sing 412 n n N1 C2 TYD sing 413 n y N1 C6 TYD sing 414 n y C2 O2 TYD doub 415 n n C2 N3 TYD sing 416 n y N3 C4 TYD sing 417 n y N3 HN3 TYD sing 418 n n C4 O4 TYD doub 419 n n C4 C5 TYD sing 420 n y C5 C5M TYD sing 421 n n C5 C6 TYD doub 422 n y C5M H51 TYD sing 423 n n C5M H52 TYD sing 424 n n C5M H53 TYD sing 425 n n C6 H6 TYD sing 426 n n # _atom_sites.entry_id 1N5J _atom_sites.fract_transf_matrix[1][1] 0.013115 _atom_sites.fract_transf_matrix[1][2] 0.007572 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015144 _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] 0.007401 _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 1 215 209 SO4 SO4 . C 2 SO4 A 1 216 210 SO4 SO4 . D 3 MG A 1 217 211 MG MG . E 4 TYD A 1 218 213 TYD TYD . F 5 TTP A 1 219 214 TTP TTP . G 6 HOH A 1 1001 1001 HOH HOH . G 6 HOH A 2 1002 1002 HOH HOH . G 6 HOH A 3 1003 1003 HOH HOH . G 6 HOH A 4 1004 1004 HOH HOH . G 6 HOH A 5 1006 1006 HOH HOH . G 6 HOH A 6 1007 1007 HOH HOH . G 6 HOH A 7 1008 1008 HOH HOH . G 6 HOH A 8 1009 1009 HOH HOH . G 6 HOH A 9 1010 1010 HOH HOH . G 6 HOH A 10 1011 1011 HOH HOH . G 6 HOH A 11 1012 1012 HOH HOH . G 6 HOH A 12 1013 1013 HOH HOH . G 6 HOH A 13 1014 1014 HOH HOH . G 6 HOH A 14 1015 1015 HOH HOH . G 6 HOH A 15 1016 1016 HOH HOH . G 6 HOH A 16 1017 1017 HOH HOH . G 6 HOH A 17 1018 1018 HOH HOH . G 6 HOH A 18 1020 1020 HOH HOH . G 6 HOH A 19 1021 1021 HOH HOH . G 6 HOH A 20 1022 1022 HOH HOH . G 6 HOH A 21 1023 1023 HOH HOH . G 6 HOH A 22 1024 1024 HOH HOH . G 6 HOH A 23 1025 1025 HOH HOH . G 6 HOH A 24 1026 1026 HOH HOH . G 6 HOH A 25 1027 1027 HOH HOH . G 6 HOH A 26 1028 1028 HOH HOH . G 6 HOH A 27 1029 1029 HOH HOH . G 6 HOH A 28 1030 1030 HOH HOH . G 6 HOH A 29 1032 1032 HOH HOH . G 6 HOH A 30 1033 1033 HOH HOH . G 6 HOH A 31 1034 1034 HOH HOH . G 6 HOH A 32 1035 1035 HOH HOH . G 6 HOH A 33 1036 1036 HOH HOH . G 6 HOH A 34 1038 1038 HOH HOH . G 6 HOH A 35 1039 1039 HOH HOH . G 6 HOH A 36 1040 1040 HOH HOH . G 6 HOH A 37 1041 1041 HOH HOH . G 6 HOH A 38 1042 1042 HOH HOH . G 6 HOH A 39 1043 1043 HOH HOH . G 6 HOH A 40 1044 1044 HOH HOH . G 6 HOH A 41 1045 1045 HOH HOH . G 6 HOH A 42 1046 1046 HOH HOH . G 6 HOH A 43 1047 1047 HOH HOH . G 6 HOH A 44 1048 1048 HOH HOH . G 6 HOH A 45 1049 1049 HOH HOH . G 6 HOH A 46 1051 1051 HOH HOH . G 6 HOH A 47 1052 1052 HOH HOH . G 6 HOH A 48 1053 1053 HOH HOH . G 6 HOH A 49 1054 1054 HOH HOH . G 6 HOH A 50 1055 1055 HOH HOH . G 6 HOH A 51 1056 1056 HOH HOH . G 6 HOH A 52 1057 1057 HOH HOH . G 6 HOH A 53 1058 1058 HOH HOH . G 6 HOH A 54 1059 1059 HOH HOH . G 6 HOH A 55 1060 1060 HOH HOH . G 6 HOH A 56 1061 1061 HOH HOH . G 6 HOH A 57 1062 1062 HOH HOH . G 6 HOH A 58 1063 1063 HOH HOH . G 6 HOH A 59 1064 1064 HOH HOH . G 6 HOH A 60 1065 1065 HOH HOH . G 6 HOH A 61 1066 1066 HOH HOH . G 6 HOH A 62 1067 1067 HOH HOH . G 6 HOH A 63 1068 1068 HOH HOH . G 6 HOH A 64 1070 1070 HOH HOH . G 6 HOH A 65 1071 1071 HOH HOH . G 6 HOH A 66 1072 1072 HOH HOH . G 6 HOH A 67 1073 1073 HOH HOH . G 6 HOH A 68 1074 1074 HOH HOH . G 6 HOH A 69 1075 1075 HOH HOH . G 6 HOH A 70 1076 1076 HOH HOH . G 6 HOH A 71 1077 1077 HOH HOH . G 6 HOH A 72 1078 1078 HOH HOH . G 6 HOH A 73 1079 1079 HOH HOH . G 6 HOH A 74 1080 1080 HOH HOH . G 6 HOH A 75 1081 1081 HOH HOH . G 6 HOH A 76 1082 1082 HOH HOH . G 6 HOH A 77 1083 1083 HOH HOH . G 6 HOH A 78 1084 1084 HOH HOH . G 6 HOH A 79 1085 1085 HOH HOH . G 6 HOH A 80 1086 1086 HOH HOH . G 6 HOH A 81 1087 1087 HOH HOH . G 6 HOH A 82 1088 1088 HOH HOH . G 6 HOH A 83 1089 1089 HOH HOH . G 6 HOH A 84 1090 1090 HOH HOH . G 6 HOH A 85 1091 1091 HOH HOH . G 6 HOH A 86 1092 1092 HOH HOH . G 6 HOH A 87 1093 1093 HOH HOH . G 6 HOH A 88 1094 1094 HOH HOH . G 6 HOH A 89 1095 1095 HOH HOH . G 6 HOH A 90 1096 1096 HOH HOH . G 6 HOH A 91 1097 1097 HOH HOH . G 6 HOH A 92 1098 1098 HOH HOH . G 6 HOH A 93 1099 1099 HOH HOH . G 6 HOH A 94 1100 1100 HOH HOH . G 6 HOH A 95 1101 1101 HOH HOH . G 6 HOH A 96 1102 1102 HOH HOH . G 6 HOH A 97 1103 1103 HOH HOH . G 6 HOH A 98 1104 1104 HOH HOH . G 6 HOH A 99 1105 1105 HOH HOH . G 6 HOH A 100 1106 1106 HOH HOH . G 6 HOH A 101 1107 1107 HOH HOH . G 6 HOH A 102 1108 1108 HOH HOH . G 6 HOH A 103 1111 1111 HOH HOH . G 6 HOH A 104 1112 1112 HOH HOH . G 6 HOH A 105 1113 1113 HOH HOH . G 6 HOH A 106 1114 1114 HOH HOH . G 6 HOH A 107 1115 1115 HOH HOH . G 6 HOH A 108 1116 1116 HOH HOH . G 6 HOH A 109 1117 1117 HOH HOH . G 6 HOH A 110 1118 1118 HOH HOH . G 6 HOH A 111 1119 1119 HOH HOH . G 6 HOH A 112 1120 1120 HOH HOH . G 6 HOH A 113 1121 1121 HOH HOH . G 6 HOH A 114 1122 1122 HOH HOH . G 6 HOH A 115 1123 1123 HOH HOH . G 6 HOH A 116 1124 1124 HOH HOH . G 6 HOH A 117 1125 1125 HOH HOH . G 6 HOH A 118 1126 1126 HOH HOH . G 6 HOH A 119 1127 1127 HOH HOH . G 6 HOH A 120 1128 1128 HOH HOH . G 6 HOH A 121 1129 1129 HOH HOH . G 6 HOH A 122 1130 1130 HOH HOH . G 6 HOH A 123 1131 1131 HOH HOH . G 6 HOH A 124 1132 1132 HOH HOH . G 6 HOH A 125 1133 1133 HOH HOH . G 6 HOH A 126 1134 1134 HOH HOH . G 6 HOH A 127 1135 1135 HOH HOH . G 6 HOH A 128 1137 1137 HOH HOH . G 6 HOH A 129 1138 1138 HOH HOH . G 6 HOH A 130 1139 1139 HOH HOH . G 6 HOH A 131 1140 1140 HOH HOH . G 6 HOH A 132 1142 1142 HOH HOH . G 6 HOH A 133 1143 1143 HOH HOH . G 6 HOH A 134 1145 1145 HOH HOH . G 6 HOH A 135 1146 1146 HOH HOH . G 6 HOH A 136 1147 1147 HOH HOH . G 6 HOH A 137 1148 1148 HOH HOH . G 6 HOH A 138 1149 1149 HOH HOH . G 6 HOH A 139 1150 1150 HOH HOH . G 6 HOH A 140 1151 1151 HOH HOH . G 6 HOH A 141 1152 1152 HOH HOH . G 6 HOH A 142 1153 1153 HOH HOH . G 6 HOH A 143 1154 1154 HOH HOH . G 6 HOH A 144 1155 1155 HOH HOH . G 6 HOH A 145 1156 1156 HOH HOH . G 6 HOH A 146 1157 1157 HOH HOH . G 6 HOH A 147 1158 1158 HOH HOH . G 6 HOH A 148 1159 1159 HOH HOH . G 6 HOH A 149 1160 1160 HOH HOH . G 6 HOH A 150 1161 1161 HOH HOH . G 6 HOH A 151 1162 1162 HOH HOH . G 6 HOH A 152 1163 1163 HOH HOH . G 6 HOH A 153 1169 1169 HOH HOH . G 6 HOH A 154 1234 1234 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 PA TYD . A . E 4 26.148 14.901 8.279 0.54 12.43 ? PA TYD 218 A 1 HETATM 2 O O1A TYD . A . E 4 27.367 14.875 9.181 0.54 12.54 ? O1A TYD 218 A 1 HETATM 3 O O2A TYD . A . E 4 24.964 15.627 8.695 0.54 12.33 ? O2A TYD 218 A 1 HETATM 4 O O3A TYD . A . E 4 26.571 15.482 6.838 0.54 12.41 ? O3A TYD 218 A 1 HETATM 5 P PB TYD . A . E 4 26.08 16.726 5.914 0.54 12.09 ? PB TYD 218 A 1 HETATM 6 O O1B TYD . A . E 4 27.116 17.743 6.154 0.54 14.09 ? O1B TYD 218 A 1 HETATM 7 O O2B TYD . A . E 4 24.734 17.18 6.432 0.54 12.01 ? O2B TYD 218 A 1 HETATM 8 O O3B TYD . A . E 4 26.069 16.158 4.571 0.54 12.82 ? O3B TYD 218 A 1 HETATM 9 O O5' TYD . A . E 4 25.714 13.377 7.975 0.54 12.62 ? O5' TYD 218 A 1 HETATM 10 C C5' TYD . A . E 4 24.803 13.09 6.894 0.54 12.73 ? C5' TYD 218 A 1 HETATM 11 C C4' TYD . A . E 4 23.448 12.604 7.366 0.54 12.46 ? C4' TYD 218 A 1 HETATM 12 O O4' TYD . A . E 4 23.426 11.192 7.464 0.54 12.09 ? O4' TYD 218 A 1 HETATM 13 C C3' TYD . A . E 4 22.941 13.116 8.732 0.54 12.22 ? C3' TYD 218 A 1 HETATM 14 O O3' TYD . A . E 4 21.567 13.366 8.453 0.54 14.25 ? O3' TYD 218 A 1 HETATM 15 C C2' TYD . A . E 4 23.208 11.997 9.706 0.54 12.47 ? C2' TYD 218 A 1 HETATM 16 C C1' TYD . A . E 4 23.24 10.733 8.822 0.54 12.73 ? C1' TYD 218 A 1 HETATM 17 N N1 TYD . A . E 4 24.299 9.735 9.215 0.54 10.09 ? N1 TYD 218 A 1 HETATM 18 C C2 TYD . A . E 4 23.886 8.415 9.513 0.54 9.85 ? C2 TYD 218 A 1 HETATM 19 O O2 TYD . A . E 4 22.705 8.071 9.454 0.54 12.57 ? O2 TYD 218 A 1 HETATM 20 N N3 TYD . A . E 4 24.9 7.501 9.885 0.54 12.62 ? N3 TYD 218 A 1 HETATM 21 C C4 TYD . A . E 4 26.267 7.803 9.976 0.54 12.76 ? C4 TYD 218 A 1 HETATM 22 O O4 TYD . A . E 4 27.045 6.918 10.312 0.54 12.39 ? O4 TYD 218 A 1 HETATM 23 C C5 TYD . A . E 4 26.619 9.187 9.649 0.54 12.7 ? C5 TYD 218 A 1 HETATM 24 C C5M TYD . A . E 4 28.069 9.655 9.703 0.54 12.47 ? C5M TYD 218 A 1 HETATM 25 C C6 TYD . A . E 4 25.662 10.085 9.29 0.54 11.8 ? C6 TYD 218 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #