data_9FKA
#
_model_server_result.job_id            1O4CHudCb25bHkNvJVbqOA 
_model_server_result.datetime_utc      '2025-03-06 09:41:49' 
_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          9fka 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    9FKA 
#
_exptl.entry_id    9FKA 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              785.233 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            MENAQUINONE-9 
_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            9FKA 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9FKA 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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                      4 
_struct_asym.id                             D 
_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 A NE2 HIS 18 A HIS 18 1_555 G FE HDD . A HDD 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? 
metalc ? metalc2 A OE1 GLU 396 A GLU 396 1_555 E FE HEM . A HEM 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? 
#
_chem_comp.formula           'C56 H80 O2' 
_chem_comp.formula_weight    785.233 
_chem_comp.id                MQ9 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              MENAQUINONE-9 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
C5 C5M MQ9 sing 865 n n 
C5 C4 MQ9 sing 866 n n 
C5 C6 MQ9 doub 867 n n 
C5M H5M3 MQ9 sing 868 n n 
C5M H5M2 MQ9 sing 869 n n 
C5M H5M1 MQ9 sing 870 n n 
C4 O4 MQ9 doub 871 n n 
C4 C3 MQ9 sing 872 n n 
C3 C2 MQ9 doub 873 n y 
C3 C3A MQ9 sing 874 n y 
C2 C1 MQ9 sing 875 n n 
C2 C3D MQ9 sing 876 n y 
C1 O1 MQ9 doub 877 n n 
C1 C6 MQ9 sing 878 n n 
C6 C7 MQ9 sing 879 n n 
C3A C3B MQ9 doub 880 n y 
C3A H3A MQ9 sing 881 n n 
C3B C3C MQ9 sing 882 n y 
C3B H3B MQ9 sing 883 n n 
C3C C3D MQ9 doub 884 n y 
C3C H3C MQ9 sing 885 n n 
C3D H3D MQ9 sing 886 n n 
C7 C8 MQ9 sing 887 n n 
C7 H72 MQ9 sing 888 n n 
C7 H71 MQ9 sing 889 n n 
C8 C9 MQ9 doub 890 e n 
C8 H8 MQ9 sing 891 n n 
C9 C10 MQ9 sing 892 n n 
C9 C11 MQ9 sing 893 n n 
C10 H103 MQ9 sing 894 n n 
C10 H102 MQ9 sing 895 n n 
C10 H101 MQ9 sing 896 n n 
C11 C12 MQ9 sing 897 n n 
C11 H112 MQ9 sing 898 n n 
C11 H111 MQ9 sing 899 n n 
C12 C13 MQ9 sing 900 n n 
C12 H121 MQ9 sing 901 n n 
C12 H122 MQ9 sing 902 n n 
C13 C14 MQ9 doub 903 e n 
C13 H13 MQ9 sing 904 n n 
C14 C15 MQ9 sing 905 n n 
C14 C16 MQ9 sing 906 n n 
C15 H153 MQ9 sing 907 n n 
C15 H152 MQ9 sing 908 n n 
C15 H151 MQ9 sing 909 n n 
C16 C17 MQ9 sing 910 n n 
C16 H162 MQ9 sing 911 n n 
C16 H161 MQ9 sing 912 n n 
C17 C18 MQ9 sing 913 n n 
C17 H172 MQ9 sing 914 n n 
C17 H171 MQ9 sing 915 n n 
C18 C19 MQ9 doub 916 e n 
C18 H18 MQ9 sing 917 n n 
C19 C20 MQ9 sing 918 n n 
C19 C21 MQ9 sing 919 n n 
C20 H203 MQ9 sing 920 n n 
C20 H202 MQ9 sing 921 n n 
C20 H201 MQ9 sing 922 n n 
C21 C22 MQ9 sing 923 n n 
C21 H212 MQ9 sing 924 n n 
C21 H211 MQ9 sing 925 n n 
C22 C23 MQ9 sing 926 n n 
C22 H222 MQ9 sing 927 n n 
C22 H221 MQ9 sing 928 n n 
C23 C24 MQ9 doub 929 e n 
C23 H23 MQ9 sing 930 n n 
C24 C25 MQ9 sing 931 n n 
C24 C26 MQ9 sing 932 n n 
C25 H253 MQ9 sing 933 n n 
C25 H252 MQ9 sing 934 n n 
C25 H251 MQ9 sing 935 n n 
C26 C27 MQ9 sing 936 n n 
C26 H262 MQ9 sing 937 n n 
C26 H261 MQ9 sing 938 n n 
C27 C28 MQ9 sing 939 n n 
C27 H272 MQ9 sing 940 n n 
C27 H271 MQ9 sing 941 n n 
C28 C29 MQ9 doub 942 e n 
C28 H28 MQ9 sing 943 n n 
C29 C30 MQ9 sing 944 n n 
C29 C31 MQ9 sing 945 n n 
C30 H303 MQ9 sing 946 n n 
C30 H302 MQ9 sing 947 n n 
C30 H301 MQ9 sing 948 n n 
C31 C32 MQ9 sing 949 n n 
C31 H312 MQ9 sing 950 n n 
C31 H311 MQ9 sing 951 n n 
C32 C33 MQ9 sing 952 n n 
C32 H321 MQ9 sing 953 n n 
C32 H322 MQ9 sing 954 n n 
C33 C34 MQ9 doub 955 e n 
C33 H33 MQ9 sing 956 n n 
C34 C35 MQ9 sing 957 n n 
C34 C36 MQ9 sing 958 n n 
C35 H353 MQ9 sing 959 n n 
C35 H352 MQ9 sing 960 n n 
C35 H351 MQ9 sing 961 n n 
C36 C37 MQ9 sing 962 n n 
C36 H362 MQ9 sing 963 n n 
C36 H361 MQ9 sing 964 n n 
C37 C38 MQ9 sing 965 n n 
C37 H372 MQ9 sing 966 n n 
C37 H371 MQ9 sing 967 n n 
C38 C39 MQ9 doub 968 z n 
C38 H38 MQ9 sing 969 n n 
C39 C40 MQ9 sing 970 n n 
C39 C41 MQ9 sing 971 n n 
C40 H403 MQ9 sing 972 n n 
C40 H402 MQ9 sing 973 n n 
C40 H401 MQ9 sing 974 n n 
C41 C42 MQ9 sing 975 n n 
C41 H412 MQ9 sing 976 n n 
C41 H411 MQ9 sing 977 n n 
C42 C43 MQ9 sing 978 n n 
C42 H422 MQ9 sing 979 n n 
C42 H421 MQ9 sing 980 n n 
C43 C44 MQ9 doub 981 e n 
C43 H43 MQ9 sing 982 n n 
C44 C45 MQ9 sing 983 n n 
C44 C46 MQ9 sing 984 n n 
C45 H453 MQ9 sing 985 n n 
C45 H452 MQ9 sing 986 n n 
C45 H451 MQ9 sing 987 n n 
C46 C47 MQ9 sing 988 n n 
C46 H462 MQ9 sing 989 n n 
C46 H461 MQ9 sing 990 n n 
C47 C48 MQ9 sing 991 n n 
C47 H472 MQ9 sing 992 n n 
C47 H471 MQ9 sing 993 n n 
C48 C49 MQ9 doub 994 n n 
C48 H48 MQ9 sing 995 n n 
C49 C50 MQ9 sing 996 n n 
C49 C51 MQ9 sing 997 n n 
C50 H503 MQ9 sing 998 n n 
C50 H502 MQ9 sing 999 n n 
C50 H501 MQ9 sing 1000 n n 
C51 H513 MQ9 sing 1001 n n 
C51 H512 MQ9 sing 1002 n n 
C51 H511 MQ9 sing 1003 n n 
#
_atom_sites.entry_id                     9FKA 
_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
C 3 PTY A 1 501 501 PTY PTY . 
D 4 MQ9 A 1 502 502 MQ9 MQ9 . 
E 5 HEM A 1 503 601 HEM HEM . 
F 5 HEM A 1 504 701 HEM HEM . 
G 6 HDD A 1 505 801 HDD HDD . 
H 7 CDL B 1 401 401 CDL CDL . 
I 8 CD4 B 1 402 402 CD4 CD4 . 
#
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 C5 MQ9 . . . D 4 118.467 119.188 124.658 1 96.98 ? C5 MQ9 502 A 1 
HETATM 2 C C5M MQ9 . . . D 4 117.738 119.281 125.963 1 92.43 ? C5M MQ9 502 A 1 
HETATM 3 C C4 MQ9 . . . D 4 119.821 119.797 124.601 1 99.08 ? C4 MQ9 502 A 1 
HETATM 4 O O4 MQ9 . . . D 4 120.299 120.339 125.577 1 104.68 ? O4 MQ9 502 A 1 
HETATM 5 C C3 MQ9 . . . D 4 120.58 119.73 123.333 1 91.38 ? C3 MQ9 502 A 1 
HETATM 6 C C2 MQ9 . . . D 4 120.027 119.108 122.218 1 84.12 ? C2 MQ9 502 A 1 
HETATM 7 C C1 MQ9 . . . D 4 118.677 118.509 122.296 1 79.53 ? C1 MQ9 502 A 1 
HETATM 8 O O1 MQ9 . . . D 4 118.185 117.965 121.332 1 76.76 ? O1 MQ9 502 A 1 
HETATM 9 C C6 MQ9 . . . D 4 117.935 118.589 123.576 1 85.73 ? C6 MQ9 502 A 1 
HETATM 10 C C3A MQ9 . . . D 4 121.848 120.292 123.258 1 94.58 ? C3A MQ9 502 A 1 
HETATM 11 C C3B MQ9 . . . D 4 122.561 120.232 122.073 1 89.13 ? C3B MQ9 502 A 1 
HETATM 12 C C3C MQ9 . . . D 4 122.009 119.611 120.962 1 90.79 ? C3C MQ9 502 A 1 
HETATM 13 C C3D MQ9 . . . D 4 120.745 119.05 121.033 1 89.01 ? C3D MQ9 502 A 1 
HETATM 14 C C7 MQ9 . . . D 4 116.572 117.96 123.591 1 81.37 ? C7 MQ9 502 A 1 
HETATM 15 C C8 MQ9 . . . D 4 115.518 119.027 123.693 1 87.63 ? C8 MQ9 502 A 1 
HETATM 16 C C9 MQ9 . . . D 4 114.356 119.095 123.044 1 89.54 ? C9 MQ9 502 A 1 
HETATM 17 C C10 MQ9 . . . D 4 113.869 118.084 122.055 1 96 ? C10 MQ9 502 A 1 
HETATM 18 C C11 MQ9 . . . D 4 113.43 120.255 123.289 1 90.99 ? C11 MQ9 502 A 1 
HETATM 19 C C12 MQ9 . . . D 4 112.84 120.845 121.998 1 95.77 ? C12 MQ9 502 A 1 
HETATM 20 C C13 MQ9 . . . D 4 111.557 120.167 121.63 1 101.29 ? C13 MQ9 502 A 1 
HETATM 21 C C14 MQ9 . . . D 4 110.373 120.724 121.367 1 106.86 ? C14 MQ9 502 A 1 
HETATM 22 C C15 MQ9 . . . D 4 110.103 122.2 121.395 1 93.56 ? C15 MQ9 502 A 1 
HETATM 23 C C16 MQ9 . . . D 4 109.194 119.86 121.013 1 104.26 ? C16 MQ9 502 A 1 
HETATM 24 C C17 MQ9 . . . D 4 107.856 120.426 121.518 1 119.98 ? C17 MQ9 502 A 1 
HETATM 25 C C18 MQ9 . . . D 4 107.678 120.179 122.981 1 131.3 ? C18 MQ9 502 A 1 
HETATM 26 C C19 MQ9 . . . D 4 106.557 119.858 123.632 1 130.54 ? C19 MQ9 502 A 1 
HETATM 27 C C20 MQ9 . . . D 4 105.216 119.68 122.979 1 118.49 ? C20 MQ9 502 A 1 
HETATM 28 C C21 MQ9 . . . D 4 106.585 119.647 125.122 1 127.91 ? C21 MQ9 502 A 1 
HETATM 29 C C22 MQ9 . . . D 4 107.986 119.297 125.645 1 124.45 ? C22 MQ9 502 A 1 
HETATM 30 C C23 MQ9 . . . D 4 108.423 117.951 125.155 1 123.07 ? C23 MQ9 502 A 1 
HETATM 31 C C24 MQ9 . . . D 4 109.444 117.211 125.594 1 117.58 ? C24 MQ9 502 A 1 
HETATM 32 C C25 MQ9 . . . D 4 109.813 115.866 125.044 1 110.54 ? C25 MQ9 502 A 1 
HETATM 33 C C26 MQ9 . . . D 4 110.32 117.713 126.709 1 113.43 ? C26 MQ9 502 A 1 
HETATM 34 C C27 MQ9 . . . D 4 111.816 117.453 126.467 1 111.77 ? C27 MQ9 502 A 1 
HETATM 35 C C28 MQ9 . . . D 4 112.33 116.374 127.366 1 97.42 ? C28 MQ9 502 A 1 
HETATM 36 C C29 MQ9 . . . D 4 113.272 116.467 128.307 1 90.17 ? C29 MQ9 502 A 1 
HETATM 37 C C30 MQ9 . . . D 4 113.73 115.33 129.168 1 87.39 ? C30 MQ9 502 A 1 
HETATM 38 C C31 MQ9 . . . D 4 113.963 117.776 128.567 1 99.18 ? C31 MQ9 502 A 1 
HETATM 39 C C32 MQ9 . . . D 4 115.35 117.622 129.206 1 90.23 ? C32 MQ9 502 A 1 
HETATM 40 C C33 MQ9 . . . D 4 115.374 118.177 130.596 1 94.83 ? C33 MQ9 502 A 1 
HETATM 41 C C34 MQ9 . . . D 4 116.151 119.155 131.065 1 94.46 ? C34 MQ9 502 A 1 
HETATM 42 C C35 MQ9 . . . D 4 117.168 119.889 130.244 1 90.34 ? C35 MQ9 502 A 1 
HETATM 43 C C36 MQ9 . . . D 4 116.051 119.6 132.502 1 96.46 ? C36 MQ9 502 A 1 
HETATM 44 C C37 MQ9 . . . D 4 114.688 119.308 133.156 1 99.35 ? C37 MQ9 502 A 1 
HETATM 45 C C38 MQ9 . . . D 4 114.538 120.016 134.472 1 106 ? C38 MQ9 502 A 1 
HETATM 46 C C39 MQ9 . . . D 4 113.771 119.639 135.498 1 109.03 ? C39 MQ9 502 A 1 
HETATM 47 C C40 MQ9 . . . D 4 113.71 120.438 136.764 1 100.33 ? C40 MQ9 502 A 1 
HETATM 48 C C41 MQ9 . . . D 4 112.916 118.4 135.468 1 106.65 ? C41 MQ9 502 A 1 
HETATM 49 C C42 MQ9 . . . D 4 113.208 117.427 136.626 1 101.37 ? C42 MQ9 502 A 1 
HETATM 50 C C43 MQ9 . . . D 4 112.069 116.47 136.798 1 104.25 ? C43 MQ9 502 A 1 
HETATM 51 C C44 MQ9 . . . D 4 111.818 115.73 137.88 1 112.01 ? C44 MQ9 502 A 1 
HETATM 52 C C45 MQ9 . . . D 4 112.679 115.757 139.114 1 107.02 ? C45 MQ9 502 A 1 
HETATM 53 C C46 MQ9 . . . D 4 110.634 114.807 137.918 1 109.77 ? C46 MQ9 502 A 1 
HETATM 54 C C47 MQ9 . . . D 4 109.648 115.191 139.033 1 104.4 ? C47 MQ9 502 A 1 
HETATM 55 C C48 MQ9 . . . D 4 108.459 114.278 139.077 1 106.17 ? C48 MQ9 502 A 1 
HETATM 56 C C49 MQ9 . . . D 4 107.99 113.476 140.046 1 122.78 ? C49 MQ9 502 A 1 
HETATM 57 C C50 MQ9 . . . D 4 109.143 113.958 140.881 1 123.26 ? C50 MQ9 502 A 1 
HETATM 58 C C51 MQ9 . . . D 4 107.818 112.749 141.347 1 126.12 ? C51 MQ9 502 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           252 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           58 
#