data_8C88 # _model_server_result.job_id Cv6-syWC6cibRpcjDcWoRQ _model_server_result.datetime_utc '2024-11-13 06:42:08' _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 8c88 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":406}' # _entry.id 8C88 # _exptl.entry_id 8C88 _exptl.method 'X-RAY DIFFRACTION' # _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 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 90 _cell.entry_id 8C88 _cell.length_a 100.91 _cell.length_b 100.91 _cell.length_c 237.02 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8C88 _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall 'P 4n 2n' _symmetry.space_group_name_H-M 'P 42 21 2' # _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,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA _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 13 _struct_asym.id Y _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 B SG CYS 214 L CYS 214 1_555 C SG CYS 19 M CYS 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc1 B NE2 HIS 190 L HIS 190 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc2 B NE2 HIS 230 L HIS 230 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc3 C NE2 HIS 219 M HIS 219 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc4 C OE1 GLU 234 M GLU 234 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? metalc ? metalc5 C OE2 GLU 234 M GLU 234 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc6 C NE2 HIS 266 M HIS 266 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? # _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 970 n n C1 C6 U10 doub 971 n n C1 C1M U10 sing 972 n n C2 C3 U10 sing 973 n n C2 O2 U10 doub 974 n n C3 C4 U10 doub 975 n n C3 O3 U10 sing 976 n n C4 C5 U10 sing 977 n n C4 O4 U10 sing 978 n n C5 C6 U10 sing 979 n n C5 O5 U10 doub 980 n n C6 C7 U10 sing 981 n n C1M H1M1 U10 sing 982 n n C1M H1M2 U10 sing 983 n n C1M H1M3 U10 sing 984 n n C3M O3 U10 sing 985 n n C3M H3M1 U10 sing 986 n n C3M H3M2 U10 sing 987 n n C3M H3M3 U10 sing 988 n n C4M O4 U10 sing 989 n n C4M H4M1 U10 sing 990 n n C4M H4M2 U10 sing 991 n n C4M H4M3 U10 sing 992 n n C7 C8 U10 sing 993 n n C7 H71 U10 sing 994 n n C7 H72 U10 sing 995 n n C8 C9 U10 doub 996 e n C8 H8 U10 sing 997 n n C9 C10 U10 sing 998 n n C9 C11 U10 sing 999 n n C10 H101 U10 sing 1000 n n C10 H102 U10 sing 1001 n n C10 H103 U10 sing 1002 n n C11 C12 U10 sing 1003 n n C11 H111 U10 sing 1004 n n C11 H112 U10 sing 1005 n n C12 C13 U10 sing 1006 n n C12 H121 U10 sing 1007 n n C12 H122 U10 sing 1008 n n C13 C14 U10 doub 1009 e n C13 H13 U10 sing 1010 n n C14 C15 U10 sing 1011 n n C14 C16 U10 sing 1012 n n C15 H151 U10 sing 1013 n n C15 H152 U10 sing 1014 n n C15 H153 U10 sing 1015 n n C16 C17 U10 sing 1016 n n C16 H161 U10 sing 1017 n n C16 H162 U10 sing 1018 n n C17 C18 U10 sing 1019 n n C17 H171 U10 sing 1020 n n C17 H172 U10 sing 1021 n n C18 C19 U10 doub 1022 e n C18 H18 U10 sing 1023 n n C19 C20 U10 sing 1024 n n C19 C21 U10 sing 1025 n n C20 H201 U10 sing 1026 n n C20 H202 U10 sing 1027 n n C20 H203 U10 sing 1028 n n C21 C22 U10 sing 1029 n n C21 H211 U10 sing 1030 n n C21 H212 U10 sing 1031 n n C22 C23 U10 sing 1032 n n C22 H221 U10 sing 1033 n n C22 H222 U10 sing 1034 n n C23 C24 U10 doub 1035 e n C23 H23 U10 sing 1036 n n C24 C25 U10 sing 1037 n n C24 C26 U10 sing 1038 n n C25 H251 U10 sing 1039 n n C25 H252 U10 sing 1040 n n C25 H253 U10 sing 1041 n n C26 C27 U10 sing 1042 n n C26 H261 U10 sing 1043 n n C26 H262 U10 sing 1044 n n C27 C28 U10 sing 1045 n n C27 H271 U10 sing 1046 n n C27 H272 U10 sing 1047 n n C28 C29 U10 doub 1048 e n C28 H28 U10 sing 1049 n n C29 C30 U10 sing 1050 n n C29 C31 U10 sing 1051 n n C30 H301 U10 sing 1052 n n C30 H302 U10 sing 1053 n n C30 H303 U10 sing 1054 n n C31 C32 U10 sing 1055 n n C31 H311 U10 sing 1056 n n C31 H312 U10 sing 1057 n n C32 C33 U10 sing 1058 n n C32 H321 U10 sing 1059 n n C32 H322 U10 sing 1060 n n C33 C34 U10 doub 1061 e n C33 H33 U10 sing 1062 n n C34 C35 U10 sing 1063 n n C34 C36 U10 sing 1064 n n C35 H351 U10 sing 1065 n n C35 H352 U10 sing 1066 n n C35 H353 U10 sing 1067 n n C36 C37 U10 sing 1068 n n C36 H361 U10 sing 1069 n n C36 H362 U10 sing 1070 n n C37 C38 U10 sing 1071 n n C37 H371 U10 sing 1072 n n C37 H372 U10 sing 1073 n n C38 C39 U10 doub 1074 e n C38 H38 U10 sing 1075 n n C39 C40 U10 sing 1076 n n C39 C41 U10 sing 1077 n n C40 H401 U10 sing 1078 n n C40 H402 U10 sing 1079 n n C40 H403 U10 sing 1080 n n C41 C42 U10 sing 1081 n n C41 H411 U10 sing 1082 n n C41 H412 U10 sing 1083 n n C42 C43 U10 sing 1084 n n C42 H421 U10 sing 1085 n n C42 H422 U10 sing 1086 n n C43 C44 U10 doub 1087 e n C43 H43 U10 sing 1088 n n C44 C45 U10 sing 1089 n n C44 C46 U10 sing 1090 n n C45 H451 U10 sing 1091 n n C45 H452 U10 sing 1092 n n C45 H453 U10 sing 1093 n n C46 C47 U10 sing 1094 n n C46 H461 U10 sing 1095 n n C46 H462 U10 sing 1096 n n C47 C48 U10 sing 1097 n n C47 H471 U10 sing 1098 n n C47 H472 U10 sing 1099 n n C48 C49 U10 doub 1100 e n C48 H48 U10 sing 1101 n n C49 C50 U10 sing 1102 n n C49 C51 U10 sing 1103 n n C50 H501 U10 sing 1104 n n C50 H502 U10 sing 1105 n n C50 H503 U10 sing 1106 n n C51 C52 U10 sing 1107 n n C51 H511 U10 sing 1108 n n C51 H512 U10 sing 1109 n n C52 C53 U10 sing 1110 n n C52 H521 U10 sing 1111 n n C52 H522 U10 sing 1112 n n C53 C54 U10 doub 1113 n n C53 H53 U10 sing 1114 n n C54 C55 U10 sing 1115 n n C54 C56 U10 sing 1116 n n C55 H551 U10 sing 1117 n n C55 H552 U10 sing 1118 n n C55 H553 U10 sing 1119 n n C56 H561 U10 sing 1120 n n C56 H562 U10 sing 1121 n n C56 H563 U10 sing 1122 n n # _atom_sites.entry_id 8C88 _atom_sites.fract_transf_matrix[1][1] 0.00991 _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] 0.00991 _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] 0.004219 _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 NKP H 1 301 301 NKP NKP . E 5 LDA H 1 302 702 LDA LDA . F 6 UNL H 1 303 802 UNL UNL . G 6 UNL H 1 304 803 UNL UNL . H 6 UNL H 1 305 804 UNL UNL . I 7 OLC L 1 501 501 OLC OLC . J 8 BCL L 1 502 302 BCL BCL . K 8 BCL L 1 503 304 BCL BCL . L 9 BPH L 1 504 402 BPH BPH . M 6 UNL L 1 505 805 UNL UNL . N 6 UNL L 1 506 807 UNL UNL . O 6 UNL L 1 507 808 UNL UNL . P 10 DIO L 1 508 40 DIO DIO . Q 11 EDO L 1 509 46 EDO EDO . R 11 EDO L 1 510 48 EDO EDO . S 11 EDO L 1 511 50 EDO EDO . T 4 NKP M 1 401 401 NKP NKP . U 8 BCL M 1 402 301 BCL BCL . V 8 BCL M 1 403 303 BCL BCL . W 9 BPH M 1 404 401 BPH BPH . X 12 FE M 1 405 500 FE FE . Y 13 U10 M 1 406 501 U10 U10 . Z 14 SPN M 1 407 600 SPN SPN . AA 5 LDA M 1 408 701 LDA LDA . BA 5 LDA M 1 409 705 LDA LDA . CA 5 LDA M 1 410 709 LDA LDA . DA 5 LDA M 1 411 710 LDA LDA . EA 6 UNL M 1 412 810 UNL UNL . FA 15 PO4 M 1 413 2 PO4 PO4 . GA 15 PO4 M 1 414 3 PO4 PO4 . HA 5 LDA M 1 415 1 LDA LDA . IA 16 HOH H 1 401 21 HOH HOH . IA 16 HOH H 2 402 18 HOH HOH . IA 16 HOH H 3 403 17 HOH HOH . JA 16 HOH L 1 601 9 HOH HOH . JA 16 HOH L 2 602 11 HOH HOH . JA 16 HOH L 3 603 10 HOH HOH . JA 16 HOH L 4 604 4 HOH HOH . JA 16 HOH L 5 605 14 HOH HOH . JA 16 HOH L 6 606 25 HOH HOH . JA 16 HOH L 7 607 5 HOH HOH . JA 16 HOH L 8 608 13 HOH HOH . KA 16 HOH M 1 501 12 HOH HOH . KA 16 HOH M 2 502 8 HOH HOH . KA 16 HOH M 3 503 2 HOH HOH . KA 16 HOH M 4 504 3 HOH HOH . KA 16 HOH M 5 505 6 HOH HOH . KA 16 HOH M 6 506 16 HOH HOH . KA 16 HOH M 7 507 1 HOH HOH . KA 16 HOH M 8 508 24 HOH HOH . KA 16 HOH M 9 509 15 HOH HOH . KA 16 HOH M 10 510 22 HOH HOH . KA 16 HOH M 11 511 7 HOH HOH . KA 16 HOH M 12 512 19 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 . . . Y 13 18.767 -33.375 -39.442 1 56.86 ? C1 U10 406 M 1 HETATM 2 C C2 U10 . . . Y 13 18.099 -33.122 -40.633 1 56.83 ? C2 U10 406 M 1 HETATM 3 C C3 U10 . . . Y 13 18.37 -33.862 -41.802 1 60.69 ? C3 U10 406 M 1 HETATM 4 C C4 U10 . . . Y 13 19.334 -34.893 -41.754 1 65.25 ? C4 U10 406 M 1 HETATM 5 C C5 U10 . . . Y 13 20.027 -35.144 -40.527 1 59.08 ? C5 U10 406 M 1 HETATM 6 C C6 U10 . . . Y 13 19.729 -34.388 -39.381 1 55.49 ? C6 U10 406 M 1 HETATM 7 C C1M U10 . . . Y 13 18.415 -32.515 -38.25 1 51.35 ? C1M U10 406 M 1 HETATM 8 C C3M U10 . . . Y 13 16.569 -33.681 -43.282 1 45.77 ? C3M U10 406 M 1 HETATM 9 C C4M U10 . . . Y 13 18.929 -36.213 -43.692 1 54.18 ? C4M U10 406 M 1 HETATM 10 C C7 U10 . . . Y 13 20.41 -34.691 -38.054 1 57.32 ? C7 U10 406 M 1 HETATM 11 C C8 U10 . . . Y 13 19.514 -35.449 -37.078 1 56.29 ? C8 U10 406 M 1 HETATM 12 C C9 U10 . . . Y 13 19.813 -36.786 -36.527 1 54.36 ? C9 U10 406 M 1 HETATM 13 C C10 U10 . . . Y 13 21.026 -37.568 -36.939 1 56.69 ? C10 U10 406 M 1 HETATM 14 C C11 U10 . . . Y 13 18.883 -37.399 -35.508 1 59.79 ? C11 U10 406 M 1 HETATM 15 C C12 U10 . . . Y 13 19.642 -37.706 -34.209 1 62.3 ? C12 U10 406 M 1 HETATM 16 C C13 U10 . . . Y 13 20.107 -36.431 -33.53 1 61.2 ? C13 U10 406 M 1 HETATM 17 C C14 U10 . . . Y 13 19.87 -36.24 -32.096 1 63.19 ? C14 U10 406 M 1 HETATM 18 C C15 U10 . . . Y 13 19.226 -37.32 -31.276 1 68.74 ? C15 U10 406 M 1 HETATM 19 C C16 U10 . . . Y 13 20.289 -34.966 -31.425 1 58.87 ? C16 U10 406 M 1 HETATM 20 C C17 U10 . . . Y 13 21.335 -35.317 -30.378 1 60.48 ? C17 U10 406 M 1 HETATM 21 C C18 U10 . . . Y 13 22.661 -35.515 -31.049 1 58.63 ? C18 U10 406 M 1 HETATM 22 C C19 U10 . . . Y 13 23.708 -36.178 -30.291 1 61.7 ? C19 U10 406 M 1 HETATM 23 C C20 U10 . . . Y 13 23.513 -36.453 -28.835 1 61.93 ? C20 U10 406 M 1 HETATM 24 C C21 U10 . . . Y 13 24.994 -36.569 -30.967 1 68.43 ? C21 U10 406 M 1 HETATM 25 C C22 U10 . . . Y 13 26.086 -35.834 -30.209 1 67.57 ? C22 U10 406 M 1 HETATM 26 C C23 U10 . . . Y 13 27.424 -36.018 -30.858 1 65.31 ? C23 U10 406 M 1 HETATM 27 C C24 U10 . . . Y 13 28.274 -34.825 -30.964 1 71.35 ? C24 U10 406 M 1 HETATM 28 C C25 U10 . . . Y 13 27.879 -33.527 -30.33 1 67.98 ? C25 U10 406 M 1 HETATM 29 C C26 U10 . . . Y 13 29.567 -34.906 -31.721 1 74.23 ? C26 U10 406 M 1 HETATM 30 C C27 U10 . . . Y 13 30.285 -36.151 -31.224 1 74.1 ? C27 U10 406 M 1 HETATM 31 C C28 U10 . . . Y 13 31.659 -35.706 -30.83 1 71.34 ? C28 U10 406 M 1 HETATM 32 C C29 U10 . . . Y 13 32.795 -36.616 -30.988 1 78.72 ? C29 U10 406 M 1 HETATM 33 C C30 U10 . . . Y 13 32.613 -38.097 -30.807 1 72.07 ? C30 U10 406 M 1 HETATM 34 C C31 U10 . . . Y 13 34.14 -36.009 -31.328 1 84.99 ? C31 U10 406 M 1 HETATM 35 C C32 U10 . . . Y 13 33.935 -34.574 -31.836 1 82.81 ? C32 U10 406 M 1 HETATM 36 C C33 U10 . . . Y 13 34.517 -34.402 -33.231 1 74.67 ? C33 U10 406 M 1 HETATM 37 C C34 U10 . . . Y 13 35.666 -33.504 -33.471 1 79.76 ? C34 U10 406 M 1 HETATM 38 C C35 U10 . . . Y 13 36.299 -32.768 -32.318 1 77.02 ? C35 U10 406 M 1 HETATM 39 C C36 U10 . . . Y 13 36.189 -33.321 -34.88 1 77.58 ? C36 U10 406 M 1 HETATM 40 C C37 U10 . . . Y 13 37.68 -32.994 -34.913 1 73.54 ? C37 U10 406 M 1 HETATM 41 C C38 U10 . . . Y 13 38.5 -34.217 -35.279 1 68.88 ? C38 U10 406 M 1 HETATM 42 C C39 U10 . . . Y 13 39.951 -34.274 -34.998 1 82.16 ? C39 U10 406 M 1 HETATM 43 C C40 U10 . . . Y 13 40.684 -35.573 -35.128 1 77.64 ? C40 U10 406 M 1 HETATM 44 C C41 U10 . . . Y 13 40.739 -33.044 -34.586 1 77.59 ? C41 U10 406 M 1 HETATM 45 O O2 U10 . . . Y 13 17.228 -32.24 -40.608 1 55.59 ? O2 U10 406 M 1 HETATM 46 O O3 U10 . . . Y 13 17.919 -33.464 -42.904 1 54.7 ? O3 U10 406 M 1 HETATM 47 O O4 U10 . . . Y 13 19.735 -35.394 -42.841 1 66.76 ? O4 U10 406 M 1 HETATM 48 O O5 U10 . . . Y 13 20.999 -35.927 -40.475 1 51.79 ? O5 U10 406 M 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 218 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 48 #