data_8IBC # _model_server_result.job_id 2MTQbxajV0asDfWDcCpGVg _model_server_result.datetime_utc '2024-10-19 20:08:15' _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 8ibc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":404}' # _entry.id 8IBC # _exptl.entry_id 8IBC _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 863.343 _entity.id 13 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description UBIQUINONE-10 _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 21-meric _pdbx_struct_assembly.oligomeric_count 21 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 13 Y N N ? 13 FA N 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 A SG CYS 338 AA CYS 338 1_555 A SG CYS 360 AA CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf2 E SG CYS 217 AE CYS 217 1_555 E SG CYS 236 AE CYS 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf3 E SG CYS 222 AE CYS 222 1_555 E SG CYS 238 AE CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf4 H SG CYS 51 AH CYS 51 1_555 H SG CYS 65 AH CYS 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 L SG CYS 338 Aa CYS 338 1_555 L SG CYS 360 Aa CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 P SG CYS 222 Ae CYS 222 1_555 P SG CYS 238 Ae CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? disulf ? disulf7 S SG CYS 35 Ah CYS 35 1_555 S SG CYS 79 Ah CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 S SG CYS 51 Ah CYS 51 1_555 S SG CYS 65 Ah CYS 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 HA C33 CDL . Ac CDL 406 1_555 JA OB7 CDL . Ag CDL 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? metalc ? metalc1 C NE2 HIS 83 AC HIS 83 1_555 V FE HEM . AC HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc2 C NE2 HIS 97 AC HIS 97 1_555 W FE HEM . AC HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc3 C NE2 HIS 182 AC HIS 182 1_555 V FE HEM . AC HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc4 C NE2 HIS 196 AC HIS 196 1_555 W FE HEM . AC HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc5 D NE2 HIS 125 AD HIS 125 1_555 AA FE HEC . AD HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc6 D SD MET 244 AD MET 244 1_555 AA FE HEC . AD HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc7 N NE2 HIS 83 Ac HIS 83 1_555 CA FE HEM . Ac HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc8 N NE2 HIS 97 Ac HIS 97 1_555 DA FE HEM . Ac HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc9 N NE2 HIS 182 Ac HIS 182 1_555 CA FE HEM . Ac HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc10 N NE2 HIS 196 Ac HIS 196 1_555 DA FE HEM . Ac HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc11 O NE2 HIS 125 Ad HIS 125 1_555 IA FE HEC . Ad HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc12 O SD MET 244 Ad MET 244 1_555 IA FE HEC . Ad HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? # _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 909 n n C1 C6 U10 doub 910 n n C1 C1M U10 sing 911 n n C2 C3 U10 sing 912 n n C2 O2 U10 doub 913 n n C3 C4 U10 doub 914 n n C3 O3 U10 sing 915 n n C4 C5 U10 sing 916 n n C4 O4 U10 sing 917 n n C5 C6 U10 sing 918 n n C5 O5 U10 doub 919 n n C6 C7 U10 sing 920 n n C1M H1M1 U10 sing 921 n n C1M H1M2 U10 sing 922 n n C1M H1M3 U10 sing 923 n n C3M O3 U10 sing 924 n n C3M H3M1 U10 sing 925 n n C3M H3M2 U10 sing 926 n n C3M H3M3 U10 sing 927 n n C4M O4 U10 sing 928 n n C4M H4M1 U10 sing 929 n n C4M H4M2 U10 sing 930 n n C4M H4M3 U10 sing 931 n n C7 C8 U10 sing 932 n n C7 H71 U10 sing 933 n n C7 H72 U10 sing 934 n n C8 C9 U10 doub 935 e n C8 H8 U10 sing 936 n n C9 C10 U10 sing 937 n n C9 C11 U10 sing 938 n n C10 H101 U10 sing 939 n n C10 H102 U10 sing 940 n n C10 H103 U10 sing 941 n n C11 C12 U10 sing 942 n n C11 H111 U10 sing 943 n n C11 H112 U10 sing 944 n n C12 C13 U10 sing 945 n n C12 H121 U10 sing 946 n n C12 H122 U10 sing 947 n n C13 C14 U10 doub 948 e n C13 H13 U10 sing 949 n n C14 C15 U10 sing 950 n n C14 C16 U10 sing 951 n n C15 H151 U10 sing 952 n n C15 H152 U10 sing 953 n n C15 H153 U10 sing 954 n n C16 C17 U10 sing 955 n n C16 H161 U10 sing 956 n n C16 H162 U10 sing 957 n n C17 C18 U10 sing 958 n n C17 H171 U10 sing 959 n n C17 H172 U10 sing 960 n n C18 C19 U10 doub 961 e n C18 H18 U10 sing 962 n n C19 C20 U10 sing 963 n n C19 C21 U10 sing 964 n n C20 H201 U10 sing 965 n n C20 H202 U10 sing 966 n n C20 H203 U10 sing 967 n n C21 C22 U10 sing 968 n n C21 H211 U10 sing 969 n n C21 H212 U10 sing 970 n n C22 C23 U10 sing 971 n n C22 H221 U10 sing 972 n n C22 H222 U10 sing 973 n n C23 C24 U10 doub 974 e n C23 H23 U10 sing 975 n n C24 C25 U10 sing 976 n n C24 C26 U10 sing 977 n n C25 H251 U10 sing 978 n n C25 H252 U10 sing 979 n n C25 H253 U10 sing 980 n n C26 C27 U10 sing 981 n n C26 H261 U10 sing 982 n n C26 H262 U10 sing 983 n n C27 C28 U10 sing 984 n n C27 H271 U10 sing 985 n n C27 H272 U10 sing 986 n n C28 C29 U10 doub 987 e n C28 H28 U10 sing 988 n n C29 C30 U10 sing 989 n n C29 C31 U10 sing 990 n n C30 H301 U10 sing 991 n n C30 H302 U10 sing 992 n n C30 H303 U10 sing 993 n n C31 C32 U10 sing 994 n n C31 H311 U10 sing 995 n n C31 H312 U10 sing 996 n n C32 C33 U10 sing 997 n n C32 H321 U10 sing 998 n n C32 H322 U10 sing 999 n n C33 C34 U10 doub 1000 e n C33 H33 U10 sing 1001 n n C34 C35 U10 sing 1002 n n C34 C36 U10 sing 1003 n n C35 H351 U10 sing 1004 n n C35 H352 U10 sing 1005 n n C35 H353 U10 sing 1006 n n C36 C37 U10 sing 1007 n n C36 H361 U10 sing 1008 n n C36 H362 U10 sing 1009 n n C37 C38 U10 sing 1010 n n C37 H371 U10 sing 1011 n n C37 H372 U10 sing 1012 n n C38 C39 U10 doub 1013 e n C38 H38 U10 sing 1014 n n C39 C40 U10 sing 1015 n n C39 C41 U10 sing 1016 n n C40 H401 U10 sing 1017 n n C40 H402 U10 sing 1018 n n C40 H403 U10 sing 1019 n n C41 C42 U10 sing 1020 n n C41 H411 U10 sing 1021 n n C41 H412 U10 sing 1022 n n C42 C43 U10 sing 1023 n n C42 H421 U10 sing 1024 n n C42 H422 U10 sing 1025 n n C43 C44 U10 doub 1026 e n C43 H43 U10 sing 1027 n n C44 C45 U10 sing 1028 n n C44 C46 U10 sing 1029 n n C45 H451 U10 sing 1030 n n C45 H452 U10 sing 1031 n n C45 H453 U10 sing 1032 n n C46 C47 U10 sing 1033 n n C46 H461 U10 sing 1034 n n C46 H462 U10 sing 1035 n n C47 C48 U10 sing 1036 n n C47 H471 U10 sing 1037 n n C47 H472 U10 sing 1038 n n C48 C49 U10 doub 1039 e n C48 H48 U10 sing 1040 n n C49 C50 U10 sing 1041 n n C49 C51 U10 sing 1042 n n C50 H501 U10 sing 1043 n n C50 H502 U10 sing 1044 n n C50 H503 U10 sing 1045 n n C51 C52 U10 sing 1046 n n C51 H511 U10 sing 1047 n n C51 H512 U10 sing 1048 n n C52 C53 U10 sing 1049 n n C52 H521 U10 sing 1050 n n C52 H522 U10 sing 1051 n n C53 C54 U10 doub 1052 n n C53 H53 U10 sing 1053 n n C54 C55 U10 sing 1054 n n C54 C56 U10 sing 1055 n n C55 H551 U10 sing 1056 n n C55 H552 U10 sing 1057 n n C55 H553 U10 sing 1058 n n C56 H561 U10 sing 1059 n n C56 H562 U10 sing 1060 n n C56 H563 U10 sing 1061 n n # _atom_sites.entry_id 8IBC _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 V 11 HEM AC 1 401 401 HEM HEM . W 11 HEM AC 1 402 402 HEM HEM . X 12 3PE AC 1 403 403 3PE 3PE . Y 13 U10 AC 1 404 505 U10 U10 . Z 14 UQ6 AC 1 405 506 UQ6 UQ6 . AA 15 HEC AD 1 401 395 HEC HEC . BA 16 CDL Aa 1 501 536 CDL CDL . CA 11 HEM Ac 1 401 401 HEM HEM . DA 11 HEM Ac 1 402 402 HEM HEM . EA 12 3PE Ac 1 403 403 3PE 3PE . FA 13 U10 Ac 1 404 505 U10 U10 . GA 14 UQ6 Ac 1 405 506 UQ6 UQ6 . HA 16 CDL Ac 1 406 102 CDL CDL . IA 15 HEC Ad 1 401 395 HEC HEC . JA 16 CDL Ag 1 101 103 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 C1 U10 . . . Y 13 120.807 171.899 200.895 1 85.19 0 C1 U10 404 AC 1 HETATM 2 C C2 U10 . . . Y 13 119.699 171.235 201.637 1 85.19 0 C2 U10 404 AC 1 HETATM 3 C C3 U10 . . . Y 13 119.617 169.754 201.638 1 85.19 0 C3 U10 404 AC 1 HETATM 4 C C4 U10 . . . Y 13 120.628 168.946 200.906 1 85.19 0 C4 U10 404 AC 1 HETATM 5 C C5 U10 . . . Y 13 121.73 169.619 200.169 1 85.19 0 C5 U10 404 AC 1 HETATM 6 C C6 U10 . . . Y 13 121.822 171.098 200.171 1 85.19 0 C6 U10 404 AC 1 HETATM 7 C C1M U10 . . . Y 13 120.941 173.394 200.869 1 85.19 0 C1M U10 404 AC 1 HETATM 8 C C3M U10 . . . Y 13 118.623 169.094 203.743 1 85.19 0 C3M U10 404 AC 1 HETATM 9 C C4M U10 . . . Y 13 121.175 166.843 201.959 1 85.19 0 C4M U10 404 AC 1 HETATM 10 C C7 U10 . . . Y 13 122.924 171.81 199.421 1 85.19 0 C7 U10 404 AC 1 HETATM 11 C C8 U10 . . . Y 13 124.288 171.276 199.776 1 85.19 0 C8 U10 404 AC 1 HETATM 12 C C9 U10 . . . Y 13 125.35 172.081 199.666 1 85.19 0 C9 U10 404 AC 1 HETATM 13 C C10 U10 . . . Y 13 126.721 171.583 200.008 1 85.19 0 C10 U10 404 AC 1 HETATM 14 C C11 U10 . . . Y 13 125.164 173.506 199.21 1 85.19 0 C11 U10 404 AC 1 HETATM 15 C C12 U10 . . . Y 13 126.423 173.935 198.475 1 85.19 0 C12 U10 404 AC 1 HETATM 16 C C13 U10 . . . Y 13 126.582 175.434 198.538 1 85.19 0 C13 U10 404 AC 1 HETATM 17 C C14 U10 . . . Y 13 127.648 175.937 199.175 1 85.19 0 C14 U10 404 AC 1 HETATM 18 C C15 U10 . . . Y 13 127.857 177.419 199.266 1 85.19 0 C15 U10 404 AC 1 HETATM 19 C C16 U10 . . . Y 13 128.647 174.998 199.809 1 85.19 0 C16 U10 404 AC 1 HETATM 20 O O2 U10 . . . Y 13 118.833 171.901 202.254 1 85.19 0 O2 U10 404 AC 1 HETATM 21 O O3 U10 . . . Y 13 118.602 169.137 202.318 1 85.19 0 O3 U10 404 AC 1 HETATM 22 O O4 U10 . . . Y 13 120.539 167.58 200.918 1 85.19 0 O4 U10 404 AC 1 HETATM 23 O O5 U10 . . . Y 13 122.586 168.951 199.556 1 85.19 0 O5 U10 404 AC 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 23 #