data_8XNO # _model_server_result.job_id '_beQiqpQa15j2etEGG-9dA' _model_server_result.datetime_utc '2025-01-03 01:39:07' _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 8xno # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"HA","auth_seq_id":401}' # _entry.id 8XNO # _exptl.entry_id 8XNO _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 795.226 _entity.id 30 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description Ubiquinone-9 _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 23-meric _pdbx_struct_assembly.oligomeric_count 23 _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,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA _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 ? _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 30 _struct_asym.id HA _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 disulf ? disulf1 Q SG CYS 36 X CYS 36 1_555 Q SG CYS 66 X CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf2 Q SG CYS 46 X CYS 46 1_555 Q SG CYS 56 X CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 Q SG CYS 78 X CYS 78 1_555 Q SG CYS 110 X CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? disulf ? disulf4 Q SG CYS 88 X CYS 88 1_555 Q SG CYS 100 X CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc1 B SG CYS 99 B CYS 99 1_555 Y FE1 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc2 B O CYS 194 B CYS 194 1_555 Y FE3 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc3 B SG CYS 194 B CYS 194 1_555 Y FE3 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc4 E SG CYS 134 E CYS 134 1_555 BA FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc5 F SG CYS 385 F CYS 385 1_555 DA FE2 SF4 . F SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? metalc ? metalc6 G O PHE 63 G PHE 63 1_555 GA FE1 FES . G FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc7 G SG CYS 75 G CYS 75 1_555 GA FE1 FES . G FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc8 G NE2 HIS 124 G HIS 124 1_555 EA FE1 SF4 . G SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc9 G SG CYS 128 G CYS 128 1_555 EA FE3 SF4 . G SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc10 G SG CYS 137 G CYS 137 1_555 EA FE4 SF4 . G SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc11 G SG CYS 182 G CYS 182 1_555 FA FE2 SF4 . G SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc12 I SG CYS 116 I CYS 116 1_555 MA FE1 SF4 . I SF4 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc13 I SG CYS 119 I CYS 119 1_555 MA FE2 SF4 . I SF4 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc14 I SG CYS 158 I CYS 158 1_555 LA FE3 SF4 . I SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc15 L SG CYS 79 R CYS 79 1_555 OA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc16 L NE2 HIS 88 R HIS 88 1_555 OA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc17 L SG CYS 104 R CYS 104 1_555 OA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc18 L SG CYS 107 R CYS 107 1_555 OA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? # _chem_comp.formula 'C54 H82 O4' _chem_comp.formula_weight 795.226 _chem_comp.id UQ9 _chem_comp.mon_nstd_flag . _chem_comp.name Ubiquinone-9 _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '2,3-dimethoxy-5-methyl-6-[(2E,6E,10E,14Z,18E,22E,26E,30Z)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,6,10,14,18 ,22,26,30,34-nonaen-1-yl]cyclohexa-2,5-diene-1,4-dione' # 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 C51 C49 UQ9 sing 1158 n n C51 H51 UQ9 sing 1159 n n C51 H51A UQ9 sing 1160 n n C51 H51B UQ9 sing 1161 n n C49 C50 UQ9 sing 1162 n n C49 C48 UQ9 doub 1163 n n C50 H50 UQ9 sing 1164 n n C50 H50A UQ9 sing 1165 n n C50 H50B UQ9 sing 1166 n n C48 C47 UQ9 sing 1167 n n C48 H48 UQ9 sing 1168 n n C47 C46 UQ9 sing 1169 n n C47 H47 UQ9 sing 1170 n n C47 H47A UQ9 sing 1171 n n C46 C44 UQ9 sing 1172 n n C46 H46 UQ9 sing 1173 n n C46 H46A UQ9 sing 1174 n n C44 C43 UQ9 doub 1175 z n C44 C45 UQ9 sing 1176 n n C45 H45 UQ9 sing 1177 n n C45 H45A UQ9 sing 1178 n n C45 H45B UQ9 sing 1179 n n C42 C43 UQ9 sing 1180 n n C43 H43 UQ9 sing 1181 n n C42 C41 UQ9 sing 1182 n n C42 H42 UQ9 sing 1183 n n C42 H42A UQ9 sing 1184 n n C41 C39 UQ9 sing 1185 n n C41 H41 UQ9 sing 1186 n n C41 H41A UQ9 sing 1187 n n C40 C39 UQ9 sing 1188 e n C39 C38 UQ9 doub 1189 n n C40 H40 UQ9 sing 1190 n n C40 H40A UQ9 sing 1191 n n C40 H40B UQ9 sing 1192 n n C38 C37 UQ9 sing 1193 n n C38 H38 UQ9 sing 1194 n n C37 C36 UQ9 sing 1195 n n C37 H37 UQ9 sing 1196 n n C37 H37A UQ9 sing 1197 n n C34 C36 UQ9 sing 1198 n n C36 H36 UQ9 sing 1199 n n C36 H36A UQ9 sing 1200 n n C33 C34 UQ9 doub 1201 n n C34 C35 UQ9 sing 1202 n n C35 H35 UQ9 sing 1203 n n C35 H35A UQ9 sing 1204 n n C35 H35B UQ9 sing 1205 e n C32 C33 UQ9 sing 1206 n n C33 H33 UQ9 sing 1207 n n C32 C31 UQ9 sing 1208 n n C32 H32 UQ9 sing 1209 n n C32 H32A UQ9 sing 1210 n n C29 C31 UQ9 sing 1211 n n C31 H31 UQ9 sing 1212 n n C31 H31A UQ9 sing 1213 n n C30 C29 UQ9 sing 1214 e n C29 C28 UQ9 doub 1215 n n C30 H30 UQ9 sing 1216 n n C30 H30A UQ9 sing 1217 n n C30 H30B UQ9 sing 1218 n n C27 C28 UQ9 sing 1219 n n C28 H28 UQ9 sing 1220 n n C27 C26 UQ9 sing 1221 n n C27 H27 UQ9 sing 1222 n n C27 H27A UQ9 sing 1223 n n C24 C26 UQ9 sing 1224 n n C26 H26 UQ9 sing 1225 n n C26 H26A UQ9 sing 1226 n n C23 C24 UQ9 doub 1227 n n C24 C25 UQ9 sing 1228 n n C25 H25 UQ9 sing 1229 n n C25 H25A UQ9 sing 1230 n n C25 H25B UQ9 sing 1231 z n C22 C23 UQ9 sing 1232 n n C23 H23 UQ9 sing 1233 n n C21 C22 UQ9 sing 1234 n n C22 H22 UQ9 sing 1235 n n C22 H22A UQ9 sing 1236 n n C19 C21 UQ9 sing 1237 n n C21 H21 UQ9 sing 1238 n n C21 H21A UQ9 sing 1239 n n C20 C19 UQ9 sing 1240 e n C19 C18 UQ9 doub 1241 n n C20 H20 UQ9 sing 1242 n n C20 H20A UQ9 sing 1243 n n C20 H20B UQ9 sing 1244 n n C17 C18 UQ9 sing 1245 n n C18 H18 UQ9 sing 1246 n n C17 C16 UQ9 sing 1247 n n C17 H17 UQ9 sing 1248 n n C17 H17A UQ9 sing 1249 n n C14 C16 UQ9 sing 1250 n n C16 H16 UQ9 sing 1251 n n C16 H16A UQ9 sing 1252 n n C13 C14 UQ9 doub 1253 n n C14 C15 UQ9 sing 1254 n n C15 H15 UQ9 sing 1255 n n C15 H15A UQ9 sing 1256 n n C15 H15B UQ9 sing 1257 e n C12 C13 UQ9 sing 1258 n n C13 H13 UQ9 sing 1259 n n C11 C12 UQ9 sing 1260 n n C12 H12 UQ9 sing 1261 n n C12 H12A UQ9 sing 1262 n n C11 C9 UQ9 sing 1263 n n C11 H11 UQ9 sing 1264 n n C11 H11A UQ9 sing 1265 n n C10 C9 UQ9 sing 1266 e n C9 C8 UQ9 doub 1267 n n C10 H10 UQ9 sing 1268 n n C10 H10A UQ9 sing 1269 n n C10 H10B UQ9 sing 1270 n n C8 C7 UQ9 sing 1271 n n C8 H8 UQ9 sing 1272 n n C7 C6 UQ9 sing 1273 n n C7 H7 UQ9 sing 1274 n n C7 H7A UQ9 sing 1275 n n C5 C6 UQ9 sing 1276 n n C6 C1 UQ9 doub 1277 n n C1 C2 UQ9 sing 1278 n n C1 C1M UQ9 sing 1279 n n C1M H1M UQ9 sing 1280 n n C1M H1MA UQ9 sing 1281 n n C1M H1MB UQ9 sing 1282 n n C3 C2 UQ9 sing 1283 n n C2 O2 UQ9 doub 1284 n n C4 C3 UQ9 doub 1285 n n C3 O3 UQ9 sing 1286 n n O3 C3M UQ9 sing 1287 n n C3M H3M UQ9 sing 1288 n n C3M H3MA UQ9 sing 1289 n n C3M H3MB UQ9 sing 1290 n n O4 C4 UQ9 sing 1291 n n C5 C4 UQ9 sing 1292 n n O4 C4M UQ9 sing 1293 n n C4M H4M UQ9 sing 1294 n n C4M H4MA UQ9 sing 1295 n n C4M H4MB UQ9 sing 1296 n n O5 C5 UQ9 doub 1297 n n # _atom_sites.entry_id 8XNO _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 X 24 3PE A 1 401 401 3PE 3PE . Y 25 SF4 B 1 301 236 SF4 SF4 . Z 26 PC1 B 1 302 406 PC1 PC1 . AA 27 UQ1 D 1 501 501 UQ1 UQ1 . BA 28 FES E 1 301 332 FES FES . CA 29 FMN F 1 501 521 FMN FMN . DA 25 SF4 F 1 502 522 SF4 SF4 . EA 25 SF4 G 1 801 824 SF4 SF4 . FA 25 SF4 G 1 802 825 SF4 SF4 . GA 28 FES G 1 803 826 FES FES . HA 30 UQ9 H 1 401 400 UQ9 UQ9 . IA 26 PC1 H 1 402 402 PC1 PC1 . JA 24 3PE I 1 301 403 3PE 3PE . KA 26 PC1 I 1 302 404 PC1 PC1 . LA 25 SF4 I 1 303 235 SF4 SF4 . MA 25 SF4 I 1 304 236 SF4 SF4 . NA 31 NDP P 1 401 536 NDP NDP . OA 32 ZN R 1 201 221 ZN ZN . PA 33 EHZ W 1 201 201 EHZ EHZ . QA 24 3PE b 1 201 201 3PE 3PE . RA 34 CDL q 1 201 405 CDL CDL . # 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 C28 UQ9 . . . HA 30 258.735 185.149 168.934 1 31.4 0 C28 UQ9 401 H 1 HETATM 2 C C27 UQ9 . . . HA 30 258.244 185.904 170.13 1 31.4 0 C27 UQ9 401 H 1 HETATM 3 C C26 UQ9 . . . HA 30 259.325 186.75 170.766 1 31.4 0 C26 UQ9 401 H 1 HETATM 4 C C24 UQ9 . . . HA 30 258.846 187.456 172.002 1 31.4 0 C24 UQ9 401 H 1 HETATM 5 C C25 UQ9 . . . HA 30 257.418 187.198 172.367 1 31.4 0 C25 UQ9 401 H 1 HETATM 6 C C23 UQ9 . . . HA 30 259.653 188.247 172.702 1 31.4 0 C23 UQ9 401 H 1 HETATM 7 C C22 UQ9 . . . HA 30 259.329 189.016 173.941 1 31.4 0 C22 UQ9 401 H 1 HETATM 8 C C21 UQ9 . . . HA 30 260.499 189.823 174.452 1 31.4 0 C21 UQ9 401 H 1 HETATM 9 C C19 UQ9 . . . HA 30 260.125 190.653 175.647 1 31.4 0 C19 UQ9 401 H 1 HETATM 10 C C20 UQ9 . . . HA 30 258.7 190.525 176.082 1 31.4 0 C20 UQ9 401 H 1 HETATM 11 C C18 UQ9 . . . HA 30 261.013 191.434 176.251 1 31.4 0 C18 UQ9 401 H 1 HETATM 12 C C17 UQ9 . . . HA 30 260.855 192.181 177.536 1 31.4 0 C17 UQ9 401 H 1 HETATM 13 C C16 UQ9 . . . HA 30 262.097 192.973 177.878 1 31.4 0 C16 UQ9 401 H 1 HETATM 14 C C14 UQ9 . . . HA 30 261.978 193.71 179.179 1 31.4 0 C14 UQ9 401 H 1 HETATM 15 C C15 UQ9 . . . HA 30 260.675 193.532 179.892 1 31.4 0 C15 UQ9 401 H 1 HETATM 16 C C13 UQ9 . . . HA 30 262.976 194.454 179.644 1 31.4 0 C13 UQ9 401 H 1 HETATM 17 C C12 UQ9 . . . HA 30 263.041 195.208 180.936 1 31.4 0 C12 UQ9 401 H 1 HETATM 18 C C11 UQ9 . . . HA 30 264.365 195.915 181.117 1 31.4 0 C11 UQ9 401 H 1 HETATM 19 C C9 UQ9 . . . HA 30 264.239 197.262 181.767 1 31.4 0 C9 UQ9 401 H 1 HETATM 20 C C10 UQ9 . . . HA 30 264.745 198.415 180.959 1 31.4 0 C10 UQ9 401 H 1 HETATM 21 C C8 UQ9 . . . HA 30 263.712 197.411 182.969 1 31.4 0 C8 UQ9 401 H 1 HETATM 22 C C7 UQ9 . . . HA 30 264.157 198.379 184.032 1 31.4 0 C7 UQ9 401 H 1 HETATM 23 C C6 UQ9 . . . HA 30 263.099 199.39 184.407 1 31.4 0 C6 UQ9 401 H 1 HETATM 24 C C1 UQ9 . . . HA 30 262.209 199.138 185.417 1 31.4 0 C1 UQ9 401 H 1 HETATM 25 C C1M UQ9 . . . HA 30 262.298 197.914 186.27 1 31.4 0 C1M UQ9 401 H 1 HETATM 26 C C2 UQ9 . . . HA 30 261.136 200.087 185.677 1 31.4 0 C2 UQ9 401 H 1 HETATM 27 O O2 UQ9 . . . HA 30 260.307 199.875 186.552 1 31.4 0 O2 UQ9 401 H 1 HETATM 28 C C3 UQ9 . . . HA 30 261.04 201.272 184.919 1 31.4 0 C3 UQ9 401 H 1 HETATM 29 O O3 UQ9 . . . HA 30 260.121 202.192 185.31 1 31.4 0 O3 UQ9 401 H 1 HETATM 30 C C3M UQ9 . . . HA 30 260.521 202.994 186.425 1 31.4 0 C3M UQ9 401 H 1 HETATM 31 C C4 UQ9 . . . HA 30 261.897 201.444 183.823 1 31.4 0 C4 UQ9 401 H 1 HETATM 32 O O4 UQ9 . . . HA 30 261.719 202.376 182.853 1 31.4 0 O4 UQ9 401 H 1 HETATM 33 C C4M UQ9 . . . HA 30 261.968 203.724 183.26 1 31.4 0 C4M UQ9 401 H 1 HETATM 34 C C5 UQ9 . . . HA 30 263.032 200.62 183.708 1 31.4 0 C5 UQ9 401 H 1 HETATM 35 O O5 UQ9 . . . HA 30 263.951 200.987 182.991 1 31.4 0 O5 UQ9 401 H 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 143 _model_server_stats.query_time_ms 395 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 35 #