data_6KHJ # _model_server_result.job_id qdtD3MU3TvQl-xx7vX3e4w _model_server_result.datetime_utc '2025-07-15 16:31:16' _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 6khj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":403}' # _entry.id 6KHJ # _exptl.entry_id 6KHJ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 749.201 _entity.id 20 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE _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 6KHJ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KHJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octadecameric _pdbx_struct_assembly.oligomeric_count 18 _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 _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 20 _struct_asym.id U _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 metalc ? metalc1 I SG CYS 63 I CYS 63 1_555 JA FE3 SF4 . I SF4 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc2 I SG CYS 66 I CYS 66 1_555 JA FE1 SF4 . I SF4 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc3 I SG CYS 69 I CYS 69 1_555 JA FE2 SF4 . I SF4 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc4 I SG CYS 73 I CYS 73 1_555 IA FE3 SF4 . I SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc5 I SG CYS 103 I CYS 103 1_555 IA FE1 SF4 . I SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc6 I SG CYS 106 I CYS 106 1_555 IA FE4 SF4 . I SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc7 I SG CYS 109 I CYS 109 1_555 IA FE2 SF4 . I SF4 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc8 I SG CYS 113 I CYS 113 1_555 JA FE4 SF4 . I SF4 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc9 K SG CYS 52 K CYS 52 1_555 KA FE3 SF4 . K SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc10 K SG CYS 53 K CYS 53 1_555 KA FE2 SF4 . K SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc11 K SG CYS 117 K CYS 117 1_555 KA FE4 SF4 . K SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc12 K SG CYS 148 K CYS 148 1_555 KA FE1 SF4 . K SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? # _chem_comp.formula 'C53 H80 O2' _chem_comp.formula_weight 749.201 _chem_comp.id PL9 _chem_comp.mon_nstd_flag . _chem_comp.name 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'PLASTOQUINONE 9' # 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 C2 C3 PL9 doub 864 n n C2 C1 PL9 sing 865 n n C2 HC2 PL9 sing 866 n n C3 C4 PL9 sing 867 n n C3 C7 PL9 sing 868 n n C4 C5 PL9 sing 869 n n C4 O1 PL9 doub 870 n n C5 C6 PL9 doub 871 n n C5 C52 PL9 sing 872 n n C6 C1 PL9 sing 873 n n C6 C53 PL9 sing 874 n n C1 O2 PL9 doub 875 n n C7 C8 PL9 sing 876 n n C7 HC71 PL9 sing 877 n n C7 HC72 PL9 sing 878 n n C8 C9 PL9 doub 879 n n C8 HC8 PL9 sing 880 n n C9 C10 PL9 sing 881 n n C9 C11 PL9 sing 882 n n C10 H101 PL9 sing 883 n n C10 H102 PL9 sing 884 n n C10 H103 PL9 sing 885 n n C11 C12 PL9 sing 886 n n C11 H111 PL9 sing 887 n n C11 H112 PL9 sing 888 n n C12 C13 PL9 sing 889 n n C12 H121 PL9 sing 890 n n C12 H122 PL9 sing 891 n n C13 C14 PL9 doub 892 n n C13 H13 PL9 sing 893 n n C14 C15 PL9 sing 894 n n C14 C16 PL9 sing 895 n n C15 H151 PL9 sing 896 n n C15 H152 PL9 sing 897 n n C15 H153 PL9 sing 898 n n C16 C17 PL9 sing 899 n n C16 H161 PL9 sing 900 n n C16 H162 PL9 sing 901 n n C17 C18 PL9 sing 902 n n C17 H171 PL9 sing 903 n n C17 H172 PL9 sing 904 n n C18 C19 PL9 doub 905 n n C18 H18 PL9 sing 906 n n C19 C20 PL9 sing 907 n n C19 C21 PL9 sing 908 n n C20 H201 PL9 sing 909 n n C20 H202 PL9 sing 910 n n C20 H203 PL9 sing 911 n n C21 C22 PL9 sing 912 n n C21 H211 PL9 sing 913 n n C21 H212 PL9 sing 914 n n C22 C23 PL9 sing 915 n n C22 H221 PL9 sing 916 n n C22 H222 PL9 sing 917 n n C23 C24 PL9 doub 918 n n C23 H23 PL9 sing 919 n n C24 C25 PL9 sing 920 n n C24 C26 PL9 sing 921 n n C25 H251 PL9 sing 922 n n C25 H252 PL9 sing 923 n n C25 H253 PL9 sing 924 n n C26 C27 PL9 sing 925 n n C26 H261 PL9 sing 926 n n C26 H262 PL9 sing 927 n n C27 C28 PL9 sing 928 n n C27 H271 PL9 sing 929 n n C27 H272 PL9 sing 930 n n C28 C29 PL9 doub 931 n n C28 H28 PL9 sing 932 n n C29 C30 PL9 sing 933 n n C29 C31 PL9 sing 934 n n C30 H301 PL9 sing 935 n n C30 H302 PL9 sing 936 n n C30 H303 PL9 sing 937 n n C31 C32 PL9 sing 938 n n C31 H311 PL9 sing 939 n n C31 H312 PL9 sing 940 n n C32 C33 PL9 sing 941 n n C32 H321 PL9 sing 942 n n C32 H322 PL9 sing 943 n n C33 C34 PL9 doub 944 n n C33 H33 PL9 sing 945 n n C34 C35 PL9 sing 946 n n C34 C36 PL9 sing 947 n n C35 H351 PL9 sing 948 n n C35 H352 PL9 sing 949 n n C35 H353 PL9 sing 950 n n C36 C37 PL9 sing 951 n n C36 H361 PL9 sing 952 n n C36 H362 PL9 sing 953 n n C37 C38 PL9 sing 954 n n C37 H371 PL9 sing 955 n n C37 H372 PL9 sing 956 n n C38 C39 PL9 doub 957 n n C38 H38 PL9 sing 958 n n C39 C40 PL9 sing 959 n n C39 C41 PL9 sing 960 n n C40 H401 PL9 sing 961 n n C40 H402 PL9 sing 962 n n C40 H403 PL9 sing 963 n n C41 C42 PL9 sing 964 n n C41 H411 PL9 sing 965 n n C41 H412 PL9 sing 966 n n C42 C43 PL9 sing 967 n n C42 H421 PL9 sing 968 n n C42 H422 PL9 sing 969 n n C43 C44 PL9 doub 970 n n C43 H43 PL9 sing 971 n n C44 C45 PL9 sing 972 n n C44 C46 PL9 sing 973 n n C45 H451 PL9 sing 974 n n C45 H452 PL9 sing 975 n n C45 H453 PL9 sing 976 n n C46 C47 PL9 sing 977 n n C46 H461 PL9 sing 978 n n C46 H462 PL9 sing 979 n n C47 C48 PL9 sing 980 n n C47 H471 PL9 sing 981 n n C47 H472 PL9 sing 982 n n C48 C49 PL9 doub 983 n n C48 H48 PL9 sing 984 n n C49 C50 PL9 sing 985 n n C49 C51 PL9 sing 986 n n C50 H501 PL9 sing 987 n n C50 H502 PL9 sing 988 n n C50 H503 PL9 sing 989 n n C51 H511 PL9 sing 990 n n C51 H512 PL9 sing 991 n n C51 H513 PL9 sing 992 n n C52 H521 PL9 sing 993 n n C52 H522 PL9 sing 994 n n C52 H523 PL9 sing 995 n n C53 H531 PL9 sing 996 n n C53 H532 PL9 sing 997 n n C53 H533 PL9 sing 998 n n # _atom_sites.entry_id 6KHJ _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 S 19 DGD A 1 401 401 DGD DGD . T 19 DGD A 1 402 402 DGD DGD . U 20 PL9 A 1 403 403 PL9 PL9 . V 21 SQD B 1 601 501 SQD SQD . W 21 SQD C 1 201 201 SQD SQD . X 22 LHG C 1 202 202 LHG LHG . Y 22 LHG D 1 601 502 LHG LHG . Z 23 BCR D 1 602 601 BCR BCR . AA 24 LMT D 1 603 603 LMT LMT . BA 23 BCR F 1 701 602 BCR BCR . CA 25 LMG F 1 702 701 LMG LMG . DA 22 LHG F 1 703 702 LHG LHG . EA 25 LMG F 1 704 703 LMG LMG . FA 22 LHG F 1 705 704 LHG LHG . GA 22 LHG F 1 706 705 LHG LHG . HA 22 LHG I 1 201 404 LHG LHG . IA 26 SF4 I 1 202 201 SF4 SF4 . JA 26 SF4 I 1 203 202 SF4 SF4 . KA 26 SF4 K 1 301 301 SF4 SF4 . LA 21 SQD N 1 201 101 SQD SQD . # 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 C2 PL9 . . . U 20 -21.407 42.912 49.106 1 56.76 ? C2 PL9 403 A 1 HETATM 2 C C3 PL9 . . . U 20 -20.977 43.58 50.218 1 56.76 ? C3 PL9 403 A 1 HETATM 3 C C4 PL9 . . . U 20 -21.71 44.709 50.717 1 56.76 ? C4 PL9 403 A 1 HETATM 4 C C5 PL9 . . . U 20 -22.904 45.107 50.019 1 56.76 ? C5 PL9 403 A 1 HETATM 5 C C6 PL9 . . . U 20 -23.334 44.427 48.9 1 56.76 ? C6 PL9 403 A 1 HETATM 6 C C1 PL9 . . . U 20 -22.588 43.302 48.413 1 56.76 ? C1 PL9 403 A 1 HETATM 7 C C7 PL9 . . . U 20 -19.756 43.135 50.877 1 56.76 ? C7 PL9 403 A 1 HETATM 8 C C8 PL9 . . . U 20 -18.551 43.974 50.605 1 56.76 ? C8 PL9 403 A 1 HETATM 9 C C9 PL9 . . . U 20 -17.673 43.692 49.639 1 56.76 ? C9 PL9 403 A 1 HETATM 10 C C10 PL9 . . . U 20 -17.094 44.72 48.758 1 56.76 ? C10 PL9 403 A 1 HETATM 11 C C11 PL9 . . . U 20 -17.475 42.268 49.242 1 56.76 ? C11 PL9 403 A 1 HETATM 12 C C12 PL9 . . . U 20 -16.369 41.64 50.103 1 56.76 ? C12 PL9 403 A 1 HETATM 13 C C13 PL9 . . . U 20 -16.939 40.392 50.67 1 56.76 ? C13 PL9 403 A 1 HETATM 14 C C14 PL9 . . . U 20 -17.728 40.379 51.746 1 56.76 ? C14 PL9 403 A 1 HETATM 15 C C15 PL9 . . . U 20 -18.7 39.29 52 1 56.76 ? C15 PL9 403 A 1 HETATM 16 C C52 PL9 . . . U 20 -23.63 46.256 50.551 1 56.76 ? C52 PL9 403 A 1 HETATM 17 C C53 PL9 . . . U 20 -24.532 44.778 48.144 1 56.76 ? C53 PL9 403 A 1 HETATM 18 O O1 PL9 . . . U 20 -21.286 45.288 51.725 1 56.76 ? O1 PL9 403 A 1 HETATM 19 O O2 PL9 . . . U 20 -22.905 42.635 47.414 1 56.76 ? O2 PL9 403 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 462 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 19 #