data_8VTJ # _model_server_result.job_id 8i0tsm0SOSbYX1OPl476sg _model_server_result.datetime_utc '2025-06-19 18:56:10' _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 8vtj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":303}' # _entry.id 8VTJ # _exptl.entry_id 8VTJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 863.343 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description UBIQUINONE-10 _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 8VTJ _cell.length_a 141.29 _cell.length_b 141.29 _cell.length_c 187.18 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VTJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,H,I,J,K,L,M,N,O,P,Q,R,S,T _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 6 _struct_asym.id F _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 covale ? covale1 C C LEU 208 M LEU 209 1_555 C N 9IJ 209 M 9IJ 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale2 C C 9IJ 209 M 9IJ 210 1_555 C N GLY 210 M GLY 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? metalc ? metalc1 B NE2 HIS 190 L HIS 190 1_555 M FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc2 B NE2 HIS 230 L HIS 230 1_555 M FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc3 C NE2 HIS 218 M HIS 219 1_555 M FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc4 C OE1 GLU 233 M GLU 234 1_555 M FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc5 C OE2 GLU 233 M GLU 234 1_555 M FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc6 C NE2 HIS 265 M HIS 266 1_555 M FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? # _chem_comp.formula 'C59 H90 O4' _chem_comp.formula_weight 863.343 _chem_comp.id U10 _chem_comp.mon_nstd_flag . _chem_comp.name UBIQUINONE-10 _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Coenzyme Q10' # 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 C1 C2 U10 sing 1078 n n C1 C6 U10 doub 1079 n n C1 C1M U10 sing 1080 n n C2 C3 U10 sing 1081 n n C2 O2 U10 doub 1082 n n C3 C4 U10 doub 1083 n n C3 O3 U10 sing 1084 n n C4 C5 U10 sing 1085 n n C4 O4 U10 sing 1086 n n C5 C6 U10 sing 1087 n n C5 O5 U10 doub 1088 n n C6 C7 U10 sing 1089 n n C1M H1M1 U10 sing 1090 n n C1M H1M2 U10 sing 1091 n n C1M H1M3 U10 sing 1092 n n C3M O3 U10 sing 1093 n n C3M H3M1 U10 sing 1094 n n C3M H3M2 U10 sing 1095 n n C3M H3M3 U10 sing 1096 n n C4M O4 U10 sing 1097 n n C4M H4M1 U10 sing 1098 n n C4M H4M2 U10 sing 1099 n n C4M H4M3 U10 sing 1100 n n C7 C8 U10 sing 1101 n n C7 H71 U10 sing 1102 n n C7 H72 U10 sing 1103 n n C8 C9 U10 doub 1104 e n C8 H8 U10 sing 1105 n n C9 C10 U10 sing 1106 n n C9 C11 U10 sing 1107 n n C10 H101 U10 sing 1108 n n C10 H102 U10 sing 1109 n n C10 H103 U10 sing 1110 n n C11 C12 U10 sing 1111 n n C11 H111 U10 sing 1112 n n C11 H112 U10 sing 1113 n n C12 C13 U10 sing 1114 n n C12 H121 U10 sing 1115 n n C12 H122 U10 sing 1116 n n C13 C14 U10 doub 1117 e n C13 H13 U10 sing 1118 n n C14 C15 U10 sing 1119 n n C14 C16 U10 sing 1120 n n C15 H151 U10 sing 1121 n n C15 H152 U10 sing 1122 n n C15 H153 U10 sing 1123 n n C16 C17 U10 sing 1124 n n C16 H161 U10 sing 1125 n n C16 H162 U10 sing 1126 n n C17 C18 U10 sing 1127 n n C17 H171 U10 sing 1128 n n C17 H172 U10 sing 1129 n n C18 C19 U10 doub 1130 e n C18 H18 U10 sing 1131 n n C19 C20 U10 sing 1132 n n C19 C21 U10 sing 1133 n n C20 H201 U10 sing 1134 n n C20 H202 U10 sing 1135 n n C20 H203 U10 sing 1136 n n C21 C22 U10 sing 1137 n n C21 H211 U10 sing 1138 n n C21 H212 U10 sing 1139 n n C22 C23 U10 sing 1140 n n C22 H221 U10 sing 1141 n n C22 H222 U10 sing 1142 n n C23 C24 U10 doub 1143 e n C23 H23 U10 sing 1144 n n C24 C25 U10 sing 1145 n n C24 C26 U10 sing 1146 n n C25 H251 U10 sing 1147 n n C25 H252 U10 sing 1148 n n C25 H253 U10 sing 1149 n n C26 C27 U10 sing 1150 n n C26 H261 U10 sing 1151 n n C26 H262 U10 sing 1152 n n C27 C28 U10 sing 1153 n n C27 H271 U10 sing 1154 n n C27 H272 U10 sing 1155 n n C28 C29 U10 doub 1156 e n C28 H28 U10 sing 1157 n n C29 C30 U10 sing 1158 n n C29 C31 U10 sing 1159 n n C30 H301 U10 sing 1160 n n C30 H302 U10 sing 1161 n n C30 H303 U10 sing 1162 n n C31 C32 U10 sing 1163 n n C31 H311 U10 sing 1164 n n C31 H312 U10 sing 1165 n n C32 C33 U10 sing 1166 n n C32 H321 U10 sing 1167 n n C32 H322 U10 sing 1168 n n C33 C34 U10 doub 1169 e n C33 H33 U10 sing 1170 n n C34 C35 U10 sing 1171 n n C34 C36 U10 sing 1172 n n C35 H351 U10 sing 1173 n n C35 H352 U10 sing 1174 n n C35 H353 U10 sing 1175 n n C36 C37 U10 sing 1176 n n C36 H361 U10 sing 1177 n n C36 H362 U10 sing 1178 n n C37 C38 U10 sing 1179 n n C37 H371 U10 sing 1180 n n C37 H372 U10 sing 1181 n n C38 C39 U10 doub 1182 e n C38 H38 U10 sing 1183 n n C39 C40 U10 sing 1184 n n C39 C41 U10 sing 1185 n n C40 H401 U10 sing 1186 n n C40 H402 U10 sing 1187 n n C40 H403 U10 sing 1188 n n C41 C42 U10 sing 1189 n n C41 H411 U10 sing 1190 n n C41 H412 U10 sing 1191 n n C42 C43 U10 sing 1192 n n C42 H421 U10 sing 1193 n n C42 H422 U10 sing 1194 n n C43 C44 U10 doub 1195 e n C43 H43 U10 sing 1196 n n C44 C45 U10 sing 1197 n n C44 C46 U10 sing 1198 n n C45 H451 U10 sing 1199 n n C45 H452 U10 sing 1200 n n C45 H453 U10 sing 1201 n n C46 C47 U10 sing 1202 n n C46 H461 U10 sing 1203 n n C46 H462 U10 sing 1204 n n C47 C48 U10 sing 1205 n n C47 H471 U10 sing 1206 n n C47 H472 U10 sing 1207 n n C48 C49 U10 doub 1208 e n C48 H48 U10 sing 1209 n n C49 C50 U10 sing 1210 n n C49 C51 U10 sing 1211 n n C50 H501 U10 sing 1212 n n C50 H502 U10 sing 1213 n n C50 H503 U10 sing 1214 n n C51 C52 U10 sing 1215 n n C51 H511 U10 sing 1216 n n C51 H512 U10 sing 1217 n n C52 C53 U10 sing 1218 n n C52 H521 U10 sing 1219 n n C52 H522 U10 sing 1220 n n C53 C54 U10 doub 1221 n n C53 H53 U10 sing 1222 n n C54 C55 U10 sing 1223 n n C54 C56 U10 sing 1224 n n C55 H551 U10 sing 1225 n n C55 H552 U10 sing 1226 n n C55 H553 U10 sing 1227 n n C56 H561 U10 sing 1228 n n C56 H562 U10 sing 1229 n n C56 H563 U10 sing 1230 n n # _atom_sites.entry_id 8VTJ _atom_sites.fract_transf_matrix[1][1] 0.007078 _atom_sites.fract_transf_matrix[1][2] 0.004086 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008173 _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] 0.005342 _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 D 4 BCL L 1 301 301 BCL BCL . E 5 BPH L 1 302 302 BPH BPH . F 6 U10 L 1 303 303 U10 U10 . G 4 BCL L 1 304 304 BCL BCL . H 7 CL L 1 305 306 CL CL . I 4 BCL M 1 401 401 BCL BCL . J 8 LDA M 1 402 402 LDA LDA . K 8 LDA M 1 403 403 LDA LDA . L 8 LDA M 1 404 405 LDA LDA . M 9 FE M 1 405 406 FE FE . N 5 BPH M 1 406 407 BPH BPH . O 10 SPO M 1 407 409 SPO SPO . P 11 CDL M 1 408 410 CDL CDL . Q 4 BCL M 1 409 305 BCL BCL . R 12 HOH H 1 301 99 HOH HOH . R 12 HOH H 2 302 33 HOH HOH . R 12 HOH H 3 303 51 HOH HOH . R 12 HOH H 4 304 17 HOH HOH . R 12 HOH H 5 305 103 HOH HOH . R 12 HOH H 6 306 114 HOH HOH . R 12 HOH H 7 307 19 HOH HOH . R 12 HOH H 8 308 78 HOH HOH . R 12 HOH H 9 309 108 HOH HOH . R 12 HOH H 10 310 122 HOH HOH . R 12 HOH H 11 311 123 HOH HOH . R 12 HOH H 12 312 71 HOH HOH . R 12 HOH H 13 313 34 HOH HOH . R 12 HOH H 14 314 74 HOH HOH . R 12 HOH H 15 315 11 HOH HOH . R 12 HOH H 16 316 121 HOH HOH . R 12 HOH H 17 317 32 HOH HOH . R 12 HOH H 18 318 31 HOH HOH . R 12 HOH H 19 319 29 HOH HOH . R 12 HOH H 20 320 25 HOH HOH . R 12 HOH H 21 321 27 HOH HOH . R 12 HOH H 22 322 109 HOH HOH . R 12 HOH H 23 323 8 HOH HOH . R 12 HOH H 24 324 119 HOH HOH . R 12 HOH H 25 325 97 HOH HOH . R 12 HOH H 26 326 112 HOH HOH . R 12 HOH H 27 327 72 HOH HOH . R 12 HOH H 28 328 53 HOH HOH . R 12 HOH H 29 329 117 HOH HOH . R 12 HOH H 30 330 30 HOH HOH . R 12 HOH H 31 331 96 HOH HOH . R 12 HOH H 32 332 116 HOH HOH . R 12 HOH H 33 333 9 HOH HOH . R 12 HOH H 34 334 115 HOH HOH . R 12 HOH H 35 335 61 HOH HOH . R 12 HOH H 36 336 100 HOH HOH . R 12 HOH H 37 337 5 HOH HOH . R 12 HOH H 38 338 120 HOH HOH . R 12 HOH H 39 339 102 HOH HOH . R 12 HOH H 40 340 106 HOH HOH . R 12 HOH H 41 341 118 HOH HOH . R 12 HOH H 42 342 98 HOH HOH . R 12 HOH H 43 343 107 HOH HOH . R 12 HOH H 44 344 68 HOH HOH . R 12 HOH H 45 345 110 HOH HOH . R 12 HOH H 46 346 75 HOH HOH . R 12 HOH H 47 347 113 HOH HOH . R 12 HOH H 48 348 73 HOH HOH . R 12 HOH H 49 349 66 HOH HOH . R 12 HOH H 50 350 95 HOH HOH . R 12 HOH H 51 351 104 HOH HOH . R 12 HOH H 52 352 101 HOH HOH . S 12 HOH L 1 401 26 HOH HOH . S 12 HOH L 2 402 4 HOH HOH . S 12 HOH L 3 403 130 HOH HOH . S 12 HOH L 4 404 10 HOH HOH . S 12 HOH L 5 405 15 HOH HOH . S 12 HOH L 6 406 7 HOH HOH . S 12 HOH L 7 407 3 HOH HOH . S 12 HOH L 8 408 2 HOH HOH . S 12 HOH L 9 409 126 HOH HOH . S 12 HOH L 10 410 125 HOH HOH . S 12 HOH L 11 411 124 HOH HOH . S 12 HOH L 12 412 105 HOH HOH . S 12 HOH L 13 413 6 HOH HOH . S 12 HOH L 14 414 138 HOH HOH . S 12 HOH L 15 415 139 HOH HOH . S 12 HOH L 16 416 50 HOH HOH . S 12 HOH L 17 417 128 HOH HOH . S 12 HOH L 18 418 131 HOH HOH . S 12 HOH L 19 419 129 HOH HOH . S 12 HOH L 20 420 127 HOH HOH . S 12 HOH L 21 421 133 HOH HOH . S 12 HOH L 22 422 132 HOH HOH . S 12 HOH L 23 423 46 HOH HOH . S 12 HOH L 24 424 134 HOH HOH . S 12 HOH L 25 425 94 HOH HOH . S 12 HOH L 26 426 24 HOH HOH . S 12 HOH L 27 427 135 HOH HOH . S 12 HOH L 28 428 38 HOH HOH . S 12 HOH L 29 429 60 HOH HOH . T 12 HOH M 1 501 140 HOH HOH . T 12 HOH M 2 502 13 HOH HOH . T 12 HOH M 3 503 93 HOH HOH . T 12 HOH M 4 504 49 HOH HOH . T 12 HOH M 5 505 84 HOH HOH . T 12 HOH M 6 506 146 HOH HOH . T 12 HOH M 7 507 145 HOH HOH . T 12 HOH M 8 508 36 HOH HOH . T 12 HOH M 9 509 18 HOH HOH . T 12 HOH M 10 510 144 HOH HOH . T 12 HOH M 11 511 92 HOH HOH . T 12 HOH M 12 512 14 HOH HOH . T 12 HOH M 13 513 47 HOH HOH . T 12 HOH M 14 514 85 HOH HOH . T 12 HOH M 15 515 64 HOH HOH . T 12 HOH M 16 516 141 HOH HOH . T 12 HOH M 17 517 1 HOH HOH . T 12 HOH M 18 518 16 HOH HOH . T 12 HOH M 19 519 59 HOH HOH . T 12 HOH M 20 520 20 HOH HOH . T 12 HOH M 21 521 91 HOH HOH . T 12 HOH M 22 522 142 HOH HOH . T 12 HOH M 23 523 23 HOH HOH . T 12 HOH M 24 524 143 HOH HOH . T 12 HOH M 25 525 137 HOH HOH . T 12 HOH M 26 526 136 HOH HOH . T 12 HOH M 27 527 87 HOH HOH . T 12 HOH M 28 528 35 HOH HOH . T 12 HOH M 29 529 88 HOH HOH . T 12 HOH M 30 530 48 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 C1 U10 . . . F 6 -35.388 44.69 -5.223 1 123.95 ? C1 U10 303 L 1 HETATM 2 C C2 U10 . . . F 6 -35.956 44.666 -3.956 1 119.45 ? C2 U10 303 L 1 HETATM 3 C C3 U10 . . . F 6 -35.467 45.488 -2.922 1 119.39 ? C3 U10 303 L 1 HETATM 4 C C4 U10 . . . F 6 -34.387 46.35 -3.168 1 115.38 ? C4 U10 303 L 1 HETATM 5 C C5 U10 . . . F 6 -33.826 46.354 -4.461 1 119.42 ? C5 U10 303 L 1 HETATM 6 C C6 U10 . . . F 6 -34.312 45.536 -5.492 1 123.8 ? C6 U10 303 L 1 HETATM 7 C C1M U10 . . . F 6 -35.95 43.788 -6.29 1 121.85 ? C1M U10 303 L 1 HETATM 8 C C3M U10 . . . F 6 -36.28 44.843 -0.86 1 102.43 ? C3M U10 303 L 1 HETATM 9 C C4M U10 . . . F 6 -33.721 47.367 -1.142 1 93.52 ? C4M U10 303 L 1 HETATM 10 C C7 U10 . . . F 6 -33.401 45.126 -6.637 1 123.05 ? C7 U10 303 L 1 HETATM 11 C C8 U10 . . . F 6 -32.889 46.301 -7.444 1 122.05 ? C8 U10 303 L 1 HETATM 12 C C9 U10 . . . F 6 -31.473 46.276 -7.84 1 118.51 ? C9 U10 303 L 1 HETATM 13 C C10 U10 . . . F 6 -30.829 44.928 -8.008 1 117.85 ? C10 U10 303 L 1 HETATM 14 C C11 U10 . . . F 6 -30.679 47.549 -8.081 1 110.87 ? C11 U10 303 L 1 HETATM 15 O O2 U10 . . . F 6 -36.919 43.916 -3.783 1 113.81 ? O2 U10 303 L 1 HETATM 16 O O3 U10 . . . F 6 -36.195 45.734 -1.95 1 116.59 ? O3 U10 303 L 1 HETATM 17 O O4 U10 . . . F 6 -34.249 47.371 -2.452 1 102.66 ? O4 U10 303 L 1 HETATM 18 O O5 U10 . . . F 6 -32.859 47.087 -4.687 1 115.17 ? O5 U10 303 L 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 360 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 18 #