data_8IB5 # _model_server_result.job_id rA9wlvFuRIE3Z0DxZprgUA _model_server_result.datetime_utc '2024-12-22 08:49:00' _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 8ib5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"HA","auth_seq_id":401}' # _entry.id 8IB5 # _exptl.entry_id 8IB5 _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 G SG CYS 64 G CYS 64 1_555 G SG CYS 75 G CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? disulf ? disulf2 Q SG CYS 36 X CYS 36 1_555 Q SG CYS 66 X CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf3 Q SG CYS 46 X CYS 46 1_555 Q SG CYS 56 X CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 Q SG CYS 78 X CYS 78 1_555 Q SG CYS 110 X CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? disulf ? disulf5 Q SG CYS 88 X CYS 88 1_555 Q SG CYS 100 X CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc1 B SG CYS 99 B CYS 99 1_555 Y FE1 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc15 L SG CYS 79 R CYS 79 1_555 OA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? 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 8IB5 _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 UQ1 B 1 302 501 UQ1 UQ1 . AA 27 PC1 B 1 303 406 PC1 PC1 . 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 27 PC1 H 1 402 402 PC1 PC1 . JA 24 3PE I 1 301 403 3PE 3PE . KA 27 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 34 CDL a 1 101 405 CDL CDL . RA 24 3PE b 1 201 201 3PE 3PE . # 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 30 259.167 185.835 168.899 1 31.4 0 C28 UQ9 401 H 1 HETATM 2 C C27 UQ9 . . . HA 30 258.798 186.262 170.287 1 31.4 0 C27 UQ9 401 H 1 HETATM 3 C C26 UQ9 . . . HA 30 259.877 187.09 170.957 1 31.4 0 C26 UQ9 401 H 1 HETATM 4 C C24 UQ9 . . . HA 30 259.44 187.708 172.255 1 31.4 0 C24 UQ9 401 H 1 HETATM 5 C C25 UQ9 . . . HA 30 257.979 187.586 172.559 1 31.4 0 C25 UQ9 401 H 1 HETATM 6 C C23 UQ9 . . . HA 30 260.31 188.316 173.058 1 31.4 0 C23 UQ9 401 H 1 HETATM 7 C C22 UQ9 . . . HA 30 260.126 189.589 173.822 1 31.4 0 C22 UQ9 401 H 1 HETATM 8 C C21 UQ9 . . . HA 30 261.301 189.906 174.724 1 31.4 0 C21 UQ9 401 H 1 HETATM 9 C C19 UQ9 . . . HA 30 260.894 190.383 176.088 1 31.4 0 C19 UQ9 401 H 1 HETATM 10 C C20 UQ9 . . . HA 30 259.452 190.174 176.431 1 31.4 0 C20 UQ9 401 H 1 HETATM 11 C C18 UQ9 . . . HA 30 261.772 190.946 176.914 1 31.4 0 C18 UQ9 401 H 1 HETATM 12 C C17 UQ9 . . . HA 30 261.495 191.856 178.069 1 31.4 0 C17 UQ9 401 H 1 HETATM 13 C C16 UQ9 . . . HA 30 262.625 192.831 178.32 1 31.4 0 C16 UQ9 401 H 1 HETATM 14 C C14 UQ9 . . . HA 30 262.584 193.43 179.698 1 31.4 0 C14 UQ9 401 H 1 HETATM 15 C C15 UQ9 . . . HA 30 261.35 193.124 180.488 1 31.4 0 C15 UQ9 401 H 1 HETATM 16 C C13 UQ9 . . . HA 30 263.586 194.171 180.163 1 31.4 0 C13 UQ9 401 H 1 HETATM 17 C C12 UQ9 . . . HA 30 263.786 194.661 181.562 1 31.4 0 C12 UQ9 401 H 1 HETATM 18 C C11 UQ9 . . . HA 30 264.979 195.579 181.692 1 31.4 0 C11 UQ9 401 H 1 HETATM 19 C C9 UQ9 . . . HA 30 264.711 196.961 181.165 1 31.4 0 C9 UQ9 401 H 1 HETATM 20 C C10 UQ9 . . . HA 30 265.396 197.302 179.878 1 31.4 0 C10 UQ9 401 H 1 HETATM 21 C C8 UQ9 . . . HA 30 263.917 197.804 181.805 1 31.4 0 C8 UQ9 401 H 1 HETATM 22 C C7 UQ9 . . . HA 30 264.105 198.36 183.189 1 31.4 0 C7 UQ9 401 H 1 HETATM 23 C C6 UQ9 . . . HA 30 262.933 198.101 184.108 1 31.4 0 C6 UQ9 401 H 1 HETATM 24 C C1 UQ9 . . . HA 30 263.02 197.18 185.114 1 31.4 0 C1 UQ9 401 H 1 HETATM 25 C C1M UQ9 . . . HA 30 264.15 196.209 185.203 1 31.4 0 C1M UQ9 401 H 1 HETATM 26 C C2 UQ9 . . . HA 30 261.986 197.141 186.139 1 31.4 0 C2 UQ9 401 H 1 HETATM 27 O O2 UQ9 . . . HA 30 262.112 196.436 187.131 1 31.4 0 O2 UQ9 401 H 1 HETATM 28 C C3 UQ9 . . . HA 30 260.826 197.928 185.997 1 31.4 0 C3 UQ9 401 H 1 HETATM 29 O O3 UQ9 . . . HA 30 259.785 197.684 186.833 1 31.4 0 O3 UQ9 401 H 1 HETATM 30 C C3M UQ9 . . . HA 30 259.788 198.455 188.037 1 31.4 0 C3M UQ9 401 H 1 HETATM 31 C C4 UQ9 . . . HA 30 260.811 198.915 185.002 1 31.4 0 C4 UQ9 401 H 1 HETATM 32 O O4 UQ9 . . . HA 30 259.974 199.982 185.007 1 31.4 0 O4 UQ9 401 H 1 HETATM 33 C C4M UQ9 . . . HA 30 260.532 201.172 185.568 1 31.4 0 C4M UQ9 401 H 1 HETATM 34 C C5 UQ9 . . . HA 30 261.728 198.822 183.939 1 31.4 0 C5 UQ9 401 H 1 HETATM 35 O O5 UQ9 . . . HA 30 261.463 199.371 182.879 1 31.4 0 O5 UQ9 401 H 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 104 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 35 #