data_8XNR # _model_server_result.job_id wLQncENZNxxr_chKw873xg _model_server_result.datetime_utc '2025-06-22 18:11:28' _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 8xnr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"HA","auth_seq_id":401}' # _entry.id 8XNR # _exptl.entry_id 8XNR _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 _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 M SG CYS 24 S CYS 24 1_555 M SG CYS 58 S CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 Q SG CYS 46 X CYS 46 1_555 Q SG CYS 56 X CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 Q SG CYS 88 X CYS 88 1_555 Q SG CYS 100 X CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc1 B SG CYS 99 B CYS 99 1_555 Y FE1 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc2 B SG CYS 194 B CYS 194 1_555 Y FE3 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc3 E SG CYS 134 E CYS 134 1_555 BA FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc4 E SG CYS 175 E CYS 175 1_555 BA FE2 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc7 G SG CYS 75 G CYS 75 1_555 GA FE1 FES . G FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc8 G NE2 HIS 124 G HIS 124 1_555 EA FE1 SF4 . G SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc9 G SG CYS 128 G CYS 128 1_555 EA FE3 SF4 . G SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc12 I SG CYS 116 I CYS 116 1_555 LA FE1 SF4 . I SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc13 I SG CYS 119 I CYS 119 1_555 LA FE2 SF4 . I SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc14 I SG CYS 158 I CYS 158 1_555 KA FE3 SF4 . I SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc15 L SG CYS 79 R CYS 79 1_555 NA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc16 L NE2 HIS 88 R HIS 88 1_555 NA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc17 L SG CYS 104 R CYS 104 1_555 NA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc18 L SG CYS 107 R CYS 107 1_555 NA 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 903 n n C51 H51 UQ9 sing 904 n n C51 H51A UQ9 sing 905 n n C51 H51B UQ9 sing 906 n n C49 C50 UQ9 sing 907 n n C49 C48 UQ9 doub 908 n n C50 H50 UQ9 sing 909 n n C50 H50A UQ9 sing 910 n n C50 H50B UQ9 sing 911 n n C48 C47 UQ9 sing 912 n n C48 H48 UQ9 sing 913 n n C47 C46 UQ9 sing 914 n n C47 H47 UQ9 sing 915 n n C47 H47A UQ9 sing 916 n n C46 C44 UQ9 sing 917 n n C46 H46 UQ9 sing 918 n n C46 H46A UQ9 sing 919 n n C44 C43 UQ9 doub 920 z n C44 C45 UQ9 sing 921 n n C45 H45 UQ9 sing 922 n n C45 H45A UQ9 sing 923 n n C45 H45B UQ9 sing 924 n n C42 C43 UQ9 sing 925 n n C43 H43 UQ9 sing 926 n n C42 C41 UQ9 sing 927 n n C42 H42 UQ9 sing 928 n n C42 H42A UQ9 sing 929 n n C41 C39 UQ9 sing 930 n n C41 H41 UQ9 sing 931 n n C41 H41A UQ9 sing 932 n n C40 C39 UQ9 sing 933 e n C39 C38 UQ9 doub 934 n n C40 H40 UQ9 sing 935 n n C40 H40A UQ9 sing 936 n n C40 H40B UQ9 sing 937 n n C38 C37 UQ9 sing 938 n n C38 H38 UQ9 sing 939 n n C37 C36 UQ9 sing 940 n n C37 H37 UQ9 sing 941 n n C37 H37A UQ9 sing 942 n n C34 C36 UQ9 sing 943 n n C36 H36 UQ9 sing 944 n n C36 H36A UQ9 sing 945 n n C33 C34 UQ9 doub 946 n n C34 C35 UQ9 sing 947 n n C35 H35 UQ9 sing 948 n n C35 H35A UQ9 sing 949 n n C35 H35B UQ9 sing 950 e n C32 C33 UQ9 sing 951 n n C33 H33 UQ9 sing 952 n n C32 C31 UQ9 sing 953 n n C32 H32 UQ9 sing 954 n n C32 H32A UQ9 sing 955 n n C29 C31 UQ9 sing 956 n n C31 H31 UQ9 sing 957 n n C31 H31A UQ9 sing 958 n n C30 C29 UQ9 sing 959 e n C29 C28 UQ9 doub 960 n n C30 H30 UQ9 sing 961 n n C30 H30A UQ9 sing 962 n n C30 H30B UQ9 sing 963 n n C27 C28 UQ9 sing 964 n n C28 H28 UQ9 sing 965 n n C27 C26 UQ9 sing 966 n n C27 H27 UQ9 sing 967 n n C27 H27A UQ9 sing 968 n n C24 C26 UQ9 sing 969 n n C26 H26 UQ9 sing 970 n n C26 H26A UQ9 sing 971 n n C23 C24 UQ9 doub 972 n n C24 C25 UQ9 sing 973 n n C25 H25 UQ9 sing 974 n n C25 H25A UQ9 sing 975 n n C25 H25B UQ9 sing 976 z n C22 C23 UQ9 sing 977 n n C23 H23 UQ9 sing 978 n n C21 C22 UQ9 sing 979 n n C22 H22 UQ9 sing 980 n n C22 H22A UQ9 sing 981 n n C19 C21 UQ9 sing 982 n n C21 H21 UQ9 sing 983 n n C21 H21A UQ9 sing 984 n n C20 C19 UQ9 sing 985 e n C19 C18 UQ9 doub 986 n n C20 H20 UQ9 sing 987 n n C20 H20A UQ9 sing 988 n n C20 H20B UQ9 sing 989 n n C17 C18 UQ9 sing 990 n n C18 H18 UQ9 sing 991 n n C17 C16 UQ9 sing 992 n n C17 H17 UQ9 sing 993 n n C17 H17A UQ9 sing 994 n n C14 C16 UQ9 sing 995 n n C16 H16 UQ9 sing 996 n n C16 H16A UQ9 sing 997 n n C13 C14 UQ9 doub 998 n n C14 C15 UQ9 sing 999 n n C15 H15 UQ9 sing 1000 n n C15 H15A UQ9 sing 1001 n n C15 H15B UQ9 sing 1002 e n C12 C13 UQ9 sing 1003 n n C13 H13 UQ9 sing 1004 n n C11 C12 UQ9 sing 1005 n n C12 H12 UQ9 sing 1006 n n C12 H12A UQ9 sing 1007 n n C11 C9 UQ9 sing 1008 n n C11 H11 UQ9 sing 1009 n n C11 H11A UQ9 sing 1010 n n C10 C9 UQ9 sing 1011 e n C9 C8 UQ9 doub 1012 n n C10 H10 UQ9 sing 1013 n n C10 H10A UQ9 sing 1014 n n C10 H10B UQ9 sing 1015 n n C8 C7 UQ9 sing 1016 n n C8 H8 UQ9 sing 1017 n n C7 C6 UQ9 sing 1018 n n C7 H7 UQ9 sing 1019 n n C7 H7A UQ9 sing 1020 n n C5 C6 UQ9 sing 1021 n n C6 C1 UQ9 doub 1022 n n C1 C2 UQ9 sing 1023 n n C1 C1M UQ9 sing 1024 n n C1M H1M UQ9 sing 1025 n n C1M H1MA UQ9 sing 1026 n n C1M H1MB UQ9 sing 1027 n n C3 C2 UQ9 sing 1028 n n C2 O2 UQ9 doub 1029 n n C4 C3 UQ9 doub 1030 n n C3 O3 UQ9 sing 1031 n n O3 C3M UQ9 sing 1032 n n C3M H3M UQ9 sing 1033 n n C3M H3MA UQ9 sing 1034 n n C3M H3MB UQ9 sing 1035 n n O4 C4 UQ9 sing 1036 n n C5 C4 UQ9 sing 1037 n n O4 C4M UQ9 sing 1038 n n C4M H4M UQ9 sing 1039 n n C4M H4MA UQ9 sing 1040 n n C4M H4MB UQ9 sing 1041 n n O5 C5 UQ9 doub 1042 n n # _atom_sites.entry_id 8XNR _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 24 3PE H 1 402 403 3PE 3PE . JA 26 PC1 I 1 301 404 PC1 PC1 . KA 25 SF4 I 1 302 235 SF4 SF4 . LA 25 SF4 I 1 303 236 SF4 SF4 . MA 31 NDP P 1 401 536 NDP NDP . NA 32 ZN R 1 201 221 ZN ZN . OA 33 EHZ W 1 201 201 EHZ EHZ . PA 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 30 259.201 186.517 170.257 1 31.4 0 C28 UQ9 401 H 1 HETATM 2 C C27 UQ9 . . . HA 30 259.698 187.596 171.169 1 31.4 0 C27 UQ9 401 H 1 HETATM 3 C C26 UQ9 . . . HA 30 260.319 187.051 172.435 1 31.4 0 C26 UQ9 401 H 1 HETATM 4 C C24 UQ9 . . . HA 30 259.927 187.833 173.658 1 31.4 0 C24 UQ9 401 H 1 HETATM 5 C C25 UQ9 . . . HA 30 258.558 187.539 174.187 1 31.4 0 C25 UQ9 401 H 1 HETATM 6 C C23 UQ9 . . . HA 30 260.753 188.726 174.196 1 31.4 0 C23 UQ9 401 H 1 HETATM 7 C C22 UQ9 . . . HA 30 260.545 190.2 174.336 1 31.4 0 C22 UQ9 401 H 1 HETATM 8 C C21 UQ9 . . . HA 30 261.117 190.739 175.627 1 31.4 0 C21 UQ9 401 H 1 HETATM 9 C C19 UQ9 . . . HA 30 260.077 190.989 176.681 1 31.4 0 C19 UQ9 401 H 1 HETATM 10 C C20 UQ9 . . . HA 30 258.859 190.121 176.596 1 31.4 0 C20 UQ9 401 H 1 HETATM 11 C C18 UQ9 . . . HA 30 260.256 191.912 177.617 1 31.4 0 C18 UQ9 401 H 1 HETATM 12 C C17 UQ9 . . . HA 30 260.875 191.739 178.966 1 31.4 0 C17 UQ9 401 H 1 HETATM 13 C C16 UQ9 . . . HA 30 260.749 192.974 179.817 1 31.4 0 C16 UQ9 401 H 1 HETATM 14 C C14 UQ9 . . . HA 30 261.987 193.824 179.79 1 31.4 0 C14 UQ9 401 H 1 HETATM 15 C C15 UQ9 . . . HA 30 262.994 193.454 178.743 1 31.4 0 C15 UQ9 401 H 1 HETATM 16 C C13 UQ9 . . . HA 30 262.144 194.83 180.643 1 31.4 0 C13 UQ9 401 H 1 HETATM 17 C C12 UQ9 . . . HA 30 263.327 195.136 181.502 1 31.4 0 C12 UQ9 401 H 1 HETATM 18 C C11 UQ9 . . . HA 30 264.286 196.12 180.875 1 31.4 0 C11 UQ9 401 H 1 HETATM 19 C C9 UQ9 . . . HA 30 264.991 196.93 181.922 1 31.4 0 C9 UQ9 401 H 1 HETATM 20 C C10 UQ9 . . . HA 30 265.889 196.151 182.83 1 31.4 0 C10 UQ9 401 H 1 HETATM 21 C C8 UQ9 . . . HA 30 264.812 198.236 182.042 1 31.4 0 C8 UQ9 401 H 1 HETATM 22 C C7 UQ9 . . . HA 30 265.147 199.078 183.243 1 31.4 0 C7 UQ9 401 H 1 HETATM 23 C C6 UQ9 . . . HA 30 263.938 199.507 184.042 1 31.4 0 C6 UQ9 401 H 1 HETATM 24 C C1 UQ9 . . . HA 30 263.289 198.639 184.876 1 31.4 0 C1 UQ9 401 H 1 HETATM 25 C C1M UQ9 . . . HA 30 263.726 197.22 185.019 1 31.4 0 C1M UQ9 401 H 1 HETATM 26 C C2 UQ9 . . . HA 30 262.15 199.1 185.663 1 31.4 0 C2 UQ9 401 H 1 HETATM 27 O O2 UQ9 . . . HA 30 261.531 198.337 186.394 1 31.4 0 O2 UQ9 401 H 1 HETATM 28 C C3 UQ9 . . . HA 30 261.751 200.444 185.595 1 31.4 0 C3 UQ9 401 H 1 HETATM 29 O O3 UQ9 . . . HA 30 260.632 200.794 186.28 1 31.4 0 O3 UQ9 401 H 1 HETATM 30 C C3M UQ9 . . . HA 30 260.847 201.138 187.651 1 31.4 0 C3M UQ9 401 H 1 HETATM 31 C C4 UQ9 . . . HA 30 262.528 201.341 184.845 1 31.4 0 C4 UQ9 401 H 1 HETATM 32 O O4 UQ9 . . . HA 30 262.429 202.688 184.955 1 31.4 0 O4 UQ9 401 H 1 HETATM 33 C C4M UQ9 . . . HA 30 263.358 203.28 185.867 1 31.4 0 C4M UQ9 401 H 1 HETATM 34 C C5 UQ9 . . . HA 30 263.483 200.838 183.934 1 31.4 0 C5 UQ9 401 H 1 HETATM 35 O O5 UQ9 . . . HA 30 263.921 201.574 183.065 1 31.4 0 O5 UQ9 401 H 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 35 #