data_3E79 # _model_server_result.job_id hmrlEA1u76_Da46_YWiSCQ _model_server_result.datetime_utc '2025-06-22 19:03:53' _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 3e79 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":551}' # _entry.id 3E79 # _exptl.entry_id 3E79 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 425.314 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'THIAMINE 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 106.81 _cell.angle_gamma 90 _cell.entry_id 3E79 _cell.length_a 50.107 _cell.length_b 69.149 _cell.length_c 60.297 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3E79 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 OD2 ASP 43 A ASP 43 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc2 A O SER 45 A SER 45 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc3 A O PRO 118 A PRO 118 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc4 A OD1 ASP 121 A ASP 121 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc5 A OD2 ASP 121 A ASP 121 1_555 E CA CA . A CA 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.874 ? metalc ? metalc6 E CA CA . A CA 601 1_555 G O HOH . A HOH 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc7 E CA CA . A CA 601 1_555 G O HOH . A HOH 1093 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? # _chem_comp.formula 'C12 H19 N4 O7 P2 S 1' _chem_comp.formula_weight 425.314 _chem_comp.id TPP _chem_comp.mon_nstd_flag . _chem_comp.name 'THIAMINE 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 N1' C2' TPP doub 326 n y N1' C6' TPP sing 327 n y C2' CM2 TPP sing 328 n n C2' N3' TPP sing 329 n y CM2 HM21 TPP sing 330 n n CM2 HM22 TPP sing 331 n n CM2 HM23 TPP sing 332 n n N3' C4' TPP doub 333 n y C4' N4' TPP sing 334 n n C4' C5' TPP sing 335 n y N4' HN41 TPP sing 336 n n N4' HN42 TPP sing 337 n n C5' C6' TPP doub 338 n y C5' C7' TPP sing 339 n n C6' H6' TPP sing 340 n n C7' N3 TPP sing 341 n n C7' "H7'1" TPP sing 342 n n C7' "H7'2" TPP sing 343 n n N3 C2 TPP doub 344 n y N3 C4 TPP sing 345 n y C2 S1 TPP sing 346 n y C2 H2 TPP sing 347 n n S1 C5 TPP sing 348 n y C5 C4 TPP doub 349 n y C5 C6 TPP sing 350 n n C4 CM4 TPP sing 351 n n CM4 HM41 TPP sing 352 n n CM4 HM42 TPP sing 353 n n CM4 HM43 TPP sing 354 n n C6 C7 TPP sing 355 n n C6 H61 TPP sing 356 n n C6 H62 TPP sing 357 n n C7 O7 TPP sing 358 n n C7 H71 TPP sing 359 n n C7 H72 TPP sing 360 n n O7 PA TPP sing 361 n n PA O1A TPP doub 362 n n PA O2A TPP sing 363 n n PA O3A TPP sing 364 n n O2A HOA2 TPP sing 365 n n O3A PB TPP sing 366 n n PB O1B TPP doub 367 n n PB O2B TPP sing 368 n n PB O3B TPP sing 369 n n O2B HOB2 TPP sing 370 n n O3B HOB3 TPP sing 371 n n # _atom_sites.entry_id 3E79 _atom_sites.fract_transf_matrix[1][1] 0.019957 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006029 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014462 _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] 0.017325 _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 I3C A 1 500 500 I3C I3C . C 2 I3C A 1 501 501 I3C I3C . D 3 TPP A 1 551 551 TPP TPP . E 4 CA A 1 601 601 CA CA . F 5 CL A 1 602 602 CL CL . 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 1005 1005 HOH HOH . G 6 HOH A 6 1006 1006 HOH HOH . G 6 HOH A 7 1007 1007 HOH HOH . G 6 HOH A 8 1008 1008 HOH HOH . G 6 HOH A 9 1009 1009 HOH HOH . G 6 HOH A 10 1010 1010 HOH HOH . G 6 HOH A 11 1011 1011 HOH HOH . G 6 HOH A 12 1012 1012 HOH HOH . G 6 HOH A 13 1013 1013 HOH HOH . G 6 HOH A 14 1014 1014 HOH HOH . G 6 HOH A 15 1015 1015 HOH HOH . G 6 HOH A 16 1016 1016 HOH HOH . G 6 HOH A 17 1017 1017 HOH HOH . G 6 HOH A 18 1018 1018 HOH HOH . G 6 HOH A 19 1019 1019 HOH HOH . G 6 HOH A 20 1020 1020 HOH HOH . G 6 HOH A 21 1021 1021 HOH HOH . G 6 HOH A 22 1022 1022 HOH HOH . G 6 HOH A 23 1023 1023 HOH HOH . G 6 HOH A 24 1024 1024 HOH HOH . G 6 HOH A 25 1025 1025 HOH HOH . G 6 HOH A 26 1026 1026 HOH HOH . G 6 HOH A 27 1027 1027 HOH HOH . G 6 HOH A 28 1028 1028 HOH HOH . G 6 HOH A 29 1029 1029 HOH HOH . G 6 HOH A 30 1030 1030 HOH HOH . G 6 HOH A 31 1031 1031 HOH HOH . G 6 HOH A 32 1032 1032 HOH HOH . G 6 HOH A 33 1033 1033 HOH HOH . G 6 HOH A 34 1034 1034 HOH HOH . G 6 HOH A 35 1035 1035 HOH HOH . G 6 HOH A 36 1036 1036 HOH HOH . G 6 HOH A 37 1037 1037 HOH HOH . G 6 HOH A 38 1038 1038 HOH HOH . G 6 HOH A 39 1039 1039 HOH HOH . G 6 HOH A 40 1040 1040 HOH HOH . G 6 HOH A 41 1041 1041 HOH HOH . G 6 HOH A 42 1042 1042 HOH HOH . G 6 HOH A 43 1043 1043 HOH HOH . G 6 HOH A 44 1044 1044 HOH HOH . G 6 HOH A 45 1045 1045 HOH HOH . G 6 HOH A 46 1046 1046 HOH HOH . G 6 HOH A 47 1047 1047 HOH HOH . G 6 HOH A 48 1048 1048 HOH HOH . G 6 HOH A 49 1049 1049 HOH HOH . G 6 HOH A 50 1050 1050 HOH HOH . G 6 HOH A 51 1051 1051 HOH HOH . G 6 HOH A 52 1052 1052 HOH HOH . G 6 HOH A 53 1053 1053 HOH HOH . G 6 HOH A 54 1054 1054 HOH HOH . G 6 HOH A 55 1055 1055 HOH HOH . G 6 HOH A 56 1056 1056 HOH HOH . G 6 HOH A 57 1057 1057 HOH HOH . G 6 HOH A 58 1058 1058 HOH HOH . G 6 HOH A 59 1059 1059 HOH HOH . G 6 HOH A 60 1060 1060 HOH HOH . G 6 HOH A 61 1061 1061 HOH HOH . G 6 HOH A 62 1062 1062 HOH HOH . G 6 HOH A 63 1063 1063 HOH HOH . G 6 HOH A 64 1064 1064 HOH HOH . G 6 HOH A 65 1065 1065 HOH HOH . G 6 HOH A 66 1066 1066 HOH HOH . G 6 HOH A 67 1067 1067 HOH HOH . G 6 HOH A 68 1068 1068 HOH HOH . G 6 HOH A 69 1069 1069 HOH HOH . G 6 HOH A 70 1070 1070 HOH HOH . G 6 HOH A 71 1071 1071 HOH HOH . G 6 HOH A 72 1072 1072 HOH HOH . G 6 HOH A 73 1073 1073 HOH HOH . G 6 HOH A 74 1074 1074 HOH HOH . G 6 HOH A 75 1075 1075 HOH HOH . G 6 HOH A 76 1076 1076 HOH HOH . G 6 HOH A 77 1077 1077 HOH HOH . G 6 HOH A 78 1078 1078 HOH HOH . G 6 HOH A 79 1079 1079 HOH HOH . G 6 HOH A 80 1080 1080 HOH HOH . G 6 HOH A 81 1081 1081 HOH HOH . G 6 HOH A 82 1082 1082 HOH HOH . G 6 HOH A 83 1083 1083 HOH HOH . G 6 HOH A 84 1084 1084 HOH HOH . G 6 HOH A 85 1085 1085 HOH HOH . G 6 HOH A 86 1086 1086 HOH HOH . G 6 HOH A 87 1087 1087 HOH HOH . G 6 HOH A 88 1088 1088 HOH HOH . G 6 HOH A 89 1089 1089 HOH HOH . G 6 HOH A 90 1090 1090 HOH HOH . G 6 HOH A 91 1091 1091 HOH HOH . G 6 HOH A 92 1092 1092 HOH HOH . G 6 HOH A 93 1093 1093 HOH HOH . G 6 HOH A 94 1095 1095 HOH HOH . G 6 HOH A 95 1096 1096 HOH HOH . G 6 HOH A 96 1097 1097 HOH HOH . G 6 HOH A 97 1098 1098 HOH HOH . G 6 HOH A 98 1099 1099 HOH HOH . G 6 HOH A 99 1100 1100 HOH HOH . G 6 HOH A 100 1101 1101 HOH HOH . G 6 HOH A 101 1102 1102 HOH HOH . G 6 HOH A 102 1103 1103 HOH HOH . G 6 HOH A 103 1104 1104 HOH HOH . G 6 HOH A 104 1105 1105 HOH HOH . G 6 HOH A 105 1106 1106 HOH HOH . G 6 HOH A 106 1107 1107 HOH HOH . G 6 HOH A 107 1108 1108 HOH HOH . G 6 HOH A 108 1109 1109 HOH HOH . G 6 HOH A 109 1110 1110 HOH HOH . G 6 HOH A 110 1111 1111 HOH HOH . G 6 HOH A 111 1112 1112 HOH HOH . G 6 HOH A 112 1113 1113 HOH HOH . G 6 HOH A 113 1114 1114 HOH HOH . G 6 HOH A 114 1115 1115 HOH HOH . G 6 HOH A 115 1116 1116 HOH HOH . G 6 HOH A 116 1117 1117 HOH HOH . G 6 HOH A 117 1118 1118 HOH HOH . G 6 HOH A 118 1119 1119 HOH HOH . G 6 HOH A 119 1120 1120 HOH HOH . G 6 HOH A 120 1121 1121 HOH HOH . G 6 HOH A 121 1122 1122 HOH HOH . G 6 HOH A 122 1123 1123 HOH HOH . G 6 HOH A 123 1124 1124 HOH HOH . G 6 HOH A 124 1125 1125 HOH HOH . G 6 HOH A 125 1126 1126 HOH HOH . G 6 HOH A 126 1127 1127 HOH HOH . G 6 HOH A 127 1128 1128 HOH HOH . G 6 HOH A 128 1129 1129 HOH HOH . G 6 HOH A 129 1130 1130 HOH HOH . G 6 HOH A 130 1131 1131 HOH HOH . G 6 HOH A 131 1132 1132 HOH HOH . G 6 HOH A 132 1133 1133 HOH HOH . G 6 HOH A 133 1134 1134 HOH HOH . G 6 HOH A 134 1135 1135 HOH HOH . G 6 HOH A 135 1136 1136 HOH HOH . G 6 HOH A 136 1137 1137 HOH HOH . G 6 HOH A 137 1138 1138 HOH HOH . G 6 HOH A 138 1139 1139 HOH HOH . G 6 HOH A 139 1140 1140 HOH HOH . G 6 HOH A 140 1141 1141 HOH HOH . G 6 HOH A 141 1142 1142 HOH HOH . G 6 HOH A 142 1143 1143 HOH HOH . G 6 HOH A 143 1144 1144 HOH HOH . G 6 HOH A 144 1145 1145 HOH HOH . G 6 HOH A 145 1146 1146 HOH HOH . G 6 HOH A 146 1147 1147 HOH HOH . G 6 HOH A 147 1148 1148 HOH HOH . G 6 HOH A 148 1149 1149 HOH HOH . G 6 HOH A 149 1150 1150 HOH HOH . G 6 HOH A 150 1151 1151 HOH HOH . G 6 HOH A 151 1152 1152 HOH HOH . G 6 HOH A 152 1153 1153 HOH HOH . G 6 HOH A 153 1154 1154 HOH HOH . G 6 HOH A 154 1155 1155 HOH HOH . G 6 HOH A 155 1156 1156 HOH HOH . G 6 HOH A 156 1157 1157 HOH HOH . G 6 HOH A 157 1158 1158 HOH HOH . G 6 HOH A 158 1159 1159 HOH HOH . G 6 HOH A 159 1160 1160 HOH HOH . G 6 HOH A 160 1161 1161 HOH HOH . G 6 HOH A 161 1162 1162 HOH HOH . G 6 HOH A 162 1163 1163 HOH HOH . G 6 HOH A 163 1164 1164 HOH HOH . G 6 HOH A 164 1165 1165 HOH HOH . G 6 HOH A 165 1166 1166 HOH HOH . G 6 HOH A 166 1167 1167 HOH HOH . G 6 HOH A 167 1168 1168 HOH HOH . G 6 HOH A 168 1169 1169 HOH HOH . G 6 HOH A 169 1170 1170 HOH HOH . G 6 HOH A 170 1171 1171 HOH HOH . G 6 HOH A 171 1172 1172 HOH HOH . G 6 HOH A 172 1173 1173 HOH HOH . G 6 HOH A 173 1174 1174 HOH HOH . G 6 HOH A 174 1175 1175 HOH HOH . G 6 HOH A 175 1176 1176 HOH HOH . G 6 HOH A 176 1177 1177 HOH HOH . G 6 HOH A 177 1178 1178 HOH HOH . G 6 HOH A 178 1179 1179 HOH HOH . G 6 HOH A 179 1180 1180 HOH HOH . G 6 HOH A 180 1181 1181 HOH HOH . G 6 HOH A 181 1182 1182 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' TPP . . . D 3 27.66 33.868 33.025 1 23.64 ? N1' TPP 551 A 1 HETATM 2 C C2' TPP . . . D 3 26.869 32.86 32.581 1 19.46 ? C2' TPP 551 A 1 HETATM 3 C CM2 TPP . . . D 3 25.4 33.115 32.256 1 22.14 ? CM2 TPP 551 A 1 HETATM 4 N N3' TPP . . . D 3 27.366 31.603 32.527 1 24.49 ? N3' TPP 551 A 1 HETATM 5 C C4' TPP . . . D 3 28.698 31.417 32.759 1 27.82 ? C4' TPP 551 A 1 HETATM 6 N N4' TPP . . . D 3 29.164 30.174 32.672 1 40.09 ? N4' TPP 551 A 1 HETATM 7 C C5' TPP . . . D 3 29.543 32.447 33.193 1 23.62 ? C5' TPP 551 A 1 HETATM 8 C C6' TPP . . . D 3 28.956 33.718 33.293 1 15.94 ? C6' TPP 551 A 1 HETATM 9 C C7' TPP . . . D 3 31.034 32.299 33.541 1 27.95 ? C7' TPP 551 A 1 HETATM 10 N N3 TPP . . . D 3 32.022 32.603 32.492 1 20.02 ? N3 TPP 551 A 1 HETATM 11 C C2 TPP . . . D 3 31.667 32.586 31.201 1 17.89 ? C2 TPP 551 A 1 HETATM 12 S S1 TPP . . . D 3 33.058 32.949 30.23 1 16.84 ? S1 TPP 551 A 1 HETATM 13 C C5 TPP . . . D 3 34.096 33.153 31.613 1 15.18 ? C5 TPP 551 A 1 HETATM 14 C C4 TPP . . . D 3 33.333 32.894 32.74 1 13.55 ? C4 TPP 551 A 1 HETATM 15 C CM4 TPP . . . D 3 33.981 32.986 34.135 1 13.79 ? CM4 TPP 551 A 1 HETATM 16 C C6 TPP . . . D 3 35.561 33.573 31.481 1 14.6 ? C6 TPP 551 A 1 HETATM 17 C C7 TPP . . . D 3 36.469 32.38 31.192 1 20.43 ? C7 TPP 551 A 1 HETATM 18 O O7 TPP . . . D 3 36.311 31.41 32.241 1 16.21 ? O7 TPP 551 A 1 HETATM 19 P PA TPP . . . D 3 36.649 29.868 32.032 1 21.42 ? PA TPP 551 A 1 HETATM 20 O O1A TPP . . . D 3 36.089 29.11 33.158 1 22.28 ? O1A TPP 551 A 1 HETATM 21 O O2A TPP . . . D 3 36.194 29.442 30.659 1 24.5 ? O2A TPP 551 A 1 HETATM 22 O O3A TPP . . . D 3 38.224 29.767 31.896 1 19.6 ? O3A TPP 551 A 1 HETATM 23 P PB TPP . . . D 3 39.234 29.623 33.099 1 15.92 ? PB TPP 551 A 1 HETATM 24 O O1B TPP . . . D 3 39.177 30.783 34.026 1 18.99 ? O1B TPP 551 A 1 HETATM 25 O O2B TPP . . . D 3 40.665 29.494 32.411 1 15.63 ? O2B TPP 551 A 1 HETATM 26 O O3B TPP . . . D 3 38.96 28.21 33.801 1 13.94 ? O3B TPP 551 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #