data_5M7K
#
_model_server_result.job_id            Ia4igjce0vgI8hPGZOFDSQ 
_model_server_result.datetime_utc      '2024-11-08 13:34:25' 
_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          5m7k 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":404}' 
#
_entry.id    5M7K 
#
_exptl.entry_id    5M7K 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              648.999 
_entity.id                          11 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            MENAQUINONE-7 
_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            5M7K 
_cell.length_a            57.9 
_cell.length_b            84.8 
_cell.length_c            384.3 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5M7K 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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                      11 
_struct_asym.id                             S 
_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
covale ? covale1 D C FME 1 D FME 1 1_555 D N TYR 2 D TYR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
metalc ? metalc1 A NE2 HIS 111 A HIS 91 1_555 E FE HEC . A HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? 
metalc ? metalc2 A NE2 HIS 144 A HIS 124 1_555 H FE HEC . A HEC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
metalc ? metalc3 A NE2 HIS 156 A HIS 136 1_555 F FE HEC . A HEC 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? 
metalc ? metalc4 A NE2 HIS 268 A HIS 248 1_555 G FE HEC . A HEC 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? 
metalc ? metalc5 A NE2 HIS 329 A HIS 309 1_555 H FE HEC . A HEC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
metalc ? metalc6 B NE2 HIS 191 B HIS 190 1_555 R FE FE2 . C FE2 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? 
metalc ? metalc7 B NE2 HIS 231 B HIS 230 1_555 R FE FE2 . C FE2 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? 
metalc ? metalc8 C NE2 HIS 218 C HIS 217 1_555 R FE FE2 . C FE2 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? 
metalc ? metalc9 C OE1 GLU 233 C GLU 232 1_555 R FE FE2 . C FE2 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? 
metalc ? metalc10 C OE2 GLU 233 C GLU 232 1_555 R FE FE2 . C FE2 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? 
metalc ? metalc11 C NE2 HIS 265 C HIS 264 1_555 R FE FE2 . C FE2 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? 
#
_chem_comp.formula           'C46 H64 O2' 
_chem_comp.formula_weight    648.999 
_chem_comp.id                MQ7 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              MENAQUINONE-7 
_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
C1 O1 MQ7 doub 815 n n 
C1 C2 MQ7 sing 816 n n 
C1 C10 MQ7 sing 817 n n 
C2 C2M MQ7 sing 818 n n 
C2 C3 MQ7 doub 819 n n 
C2M H2M1 MQ7 sing 820 n n 
C2M H2M2 MQ7 sing 821 n n 
C2M H2M3 MQ7 sing 822 n n 
C3 C4 MQ7 sing 823 n n 
C3 C11 MQ7 sing 824 n n 
C4 O4 MQ7 doub 825 n n 
C4 C5 MQ7 sing 826 n n 
C5 C6 MQ7 doub 827 n y 
C5 C10 MQ7 sing 828 n y 
C6 C7 MQ7 sing 829 n y 
C6 H6 MQ7 sing 830 n n 
C7 C8 MQ7 doub 831 n y 
C7 H7 MQ7 sing 832 n n 
C8 C9 MQ7 sing 833 n y 
C8 H8 MQ7 sing 834 n n 
C9 C10 MQ7 doub 835 n y 
C9 H9 MQ7 sing 836 n n 
C11 C12 MQ7 sing 837 n n 
C11 H111 MQ7 sing 838 n n 
C11 H112 MQ7 sing 839 n n 
C12 C13 MQ7 doub 840 e n 
C12 H12 MQ7 sing 841 n n 
C13 C14 MQ7 sing 842 n n 
C13 C15 MQ7 sing 843 n n 
C14 H141 MQ7 sing 844 n n 
C14 H142 MQ7 sing 845 n n 
C14 H143 MQ7 sing 846 n n 
C15 C16 MQ7 sing 847 n n 
C15 H151 MQ7 sing 848 n n 
C15 H152 MQ7 sing 849 n n 
C16 C17 MQ7 sing 850 n n 
C16 H161 MQ7 sing 851 n n 
C16 H162 MQ7 sing 852 n n 
C17 C18 MQ7 doub 853 e n 
C17 H17 MQ7 sing 854 n n 
C18 C19 MQ7 sing 855 n n 
C18 C20 MQ7 sing 856 n n 
C19 H191 MQ7 sing 857 n n 
C19 H192 MQ7 sing 858 n n 
C19 H193 MQ7 sing 859 n n 
C20 C21 MQ7 sing 860 n n 
C20 H201 MQ7 sing 861 n n 
C20 H202 MQ7 sing 862 n n 
C21 C22 MQ7 sing 863 n n 
C21 H211 MQ7 sing 864 n n 
C21 H212 MQ7 sing 865 n n 
C22 C23 MQ7 doub 866 e n 
C22 H22 MQ7 sing 867 n n 
C23 C24 MQ7 sing 868 n n 
C23 C25 MQ7 sing 869 n n 
C24 H241 MQ7 sing 870 n n 
C24 H242 MQ7 sing 871 n n 
C24 H243 MQ7 sing 872 n n 
C25 C26 MQ7 sing 873 n n 
C25 H251 MQ7 sing 874 n n 
C25 H252 MQ7 sing 875 n n 
C26 C27 MQ7 sing 876 n n 
C26 H261 MQ7 sing 877 n n 
C26 H262 MQ7 sing 878 n n 
C27 C28 MQ7 doub 879 e n 
C27 H27 MQ7 sing 880 n n 
C28 C29 MQ7 sing 881 n n 
C28 C30 MQ7 sing 882 n n 
C29 H291 MQ7 sing 883 n n 
C29 H292 MQ7 sing 884 n n 
C29 H293 MQ7 sing 885 n n 
C30 C31 MQ7 sing 886 n n 
C30 H301 MQ7 sing 887 n n 
C30 H302 MQ7 sing 888 n n 
C31 C32 MQ7 sing 889 n n 
C31 H311 MQ7 sing 890 n n 
C31 H312 MQ7 sing 891 n n 
C32 C33 MQ7 doub 892 e n 
C32 H32 MQ7 sing 893 n n 
C33 C34 MQ7 sing 894 n n 
C33 C35 MQ7 sing 895 n n 
C34 H341 MQ7 sing 896 n n 
C34 H342 MQ7 sing 897 n n 
C34 H343 MQ7 sing 898 n n 
C35 C36 MQ7 sing 899 n n 
C35 H351 MQ7 sing 900 n n 
C35 H352 MQ7 sing 901 n n 
C36 C37 MQ7 sing 902 n n 
C36 H361 MQ7 sing 903 n n 
C36 H362 MQ7 sing 904 n n 
C37 C38 MQ7 doub 905 e n 
C37 H37 MQ7 sing 906 n n 
C38 C39 MQ7 sing 907 n n 
C38 C40 MQ7 sing 908 n n 
C39 H391 MQ7 sing 909 n n 
C39 H392 MQ7 sing 910 n n 
C39 H393 MQ7 sing 911 n n 
C40 C41 MQ7 sing 912 n n 
C40 H401 MQ7 sing 913 n n 
C40 H402 MQ7 sing 914 n n 
C41 C42 MQ7 sing 915 n n 
C41 H411 MQ7 sing 916 n n 
C41 H412 MQ7 sing 917 n n 
C42 C43 MQ7 doub 918 n n 
C42 H42 MQ7 sing 919 n n 
C43 C44 MQ7 sing 920 n n 
C43 C45 MQ7 sing 921 n n 
C44 H441 MQ7 sing 922 n n 
C44 H442 MQ7 sing 923 n n 
C44 H443 MQ7 sing 924 n n 
C45 H451 MQ7 sing 925 n n 
C45 H452 MQ7 sing 926 n n 
C45 H453 MQ7 sing 927 n n 
#
_atom_sites.entry_id                     5M7K 
_atom_sites.fract_transf_matrix[1][1]    0.017271 
_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]    0.011792 
_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]    0.002602 
_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
E 5 HEC A 1 401 1333 HEC HEM . 
F 5 HEC A 1 402 1334 HEC HEM . 
G 5 HEC A 1 403 1335 HEC HEM . 
H 5 HEC A 1 404 1336 HEC HEM . 
I 6 DGA A 1 405 1278 DGA DGA . 
J 7 BCL B 1 301 1274 BCL BCL . 
K 7 BCL B 1 302 1275 BCL BCL . 
L 7 BCL B 1 303 1276 BCL BCL . 
M 8 BPB B 1 304 1277 BPB BPB . 
N 9 MPG B 1 305 1279 MPG MPG . 
O 9 MPG B 1 306 1280 MPG MPG . 
P 7 BCL C 1 401 1324 BCL BCL . 
Q 8 BPB C 1 402 1325 BPB BPB . 
R 10 FE2 C 1 403 1326 FE2 FE2 . 
S 11 MQ7 C 1 404 1327 MQ7 MQ7 . 
T 12 NS5 C 1 405 1328 NS5 NS5 . 
U 13 OTP C 1 406 1329 OTP OTP . 
V 9 MPG C 1 407 1330 MPG MPG . 
W 14 PO4 C 1 408 1331 PO4 PO4 . 
X 14 PO4 C 1 409 1332 PO4 PO4 . 
#
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 MQ7 . . . S 11 0.876 -10.595 30.38 1 62.74 ? C1 MQ7 404 C 1 
HETATM 2 O O1 MQ7 . . . S 11 0.316 -11.67 30.376 1 62.04 ? O1 MQ7 404 C 1 
HETATM 3 C C2 MQ7 . . . S 11 1.03 -9.832 31.658 1 63.18 ? C2 MQ7 404 C 1 
HETATM 4 C C2M MQ7 . . . S 11 0.486 -10.41 32.943 1 61.01 ? C2M MQ7 404 C 1 
HETATM 5 C C3 MQ7 . . . S 11 1.716 -8.522 31.654 1 63.63 ? C3 MQ7 404 C 1 
HETATM 6 C C4 MQ7 . . . S 11 2.245 -7.974 30.367 1 66.09 ? C4 MQ7 404 C 1 
HETATM 7 O O4 MQ7 . . . S 11 2.811 -6.897 30.341 1 64.69 ? O4 MQ7 404 C 1 
HETATM 8 C C5 MQ7 . . . S 11 2.078 -8.774 29.044 1 67.95 ? C5 MQ7 404 C 1 
HETATM 9 C C6 MQ7 . . . S 11 2.577 -8.253 27.848 1 68.69 ? C6 MQ7 404 C 1 
HETATM 10 C C7 MQ7 . . . S 11 2.43 -8.969 26.658 1 69.35 ? C7 MQ7 404 C 1 
HETATM 11 C C8 MQ7 . . . S 11 1.78 -10.214 26.663 1 71.69 ? C8 MQ7 404 C 1 
HETATM 12 C C9 MQ7 . . . S 11 1.28 -10.736 27.86 1 70.31 ? C9 MQ7 404 C 1 
HETATM 13 C C10 MQ7 . . . S 11 1.427 -10.02 29.051 1 66.81 ? C10 MQ7 404 C 1 
HETATM 14 C C11 MQ7 . . . S 11 1.884 -7.722 32.968 1 58.89 ? C11 MQ7 404 C 1 
HETATM 15 C C12 MQ7 . . . S 11 3.139 -8.2 33.694 1 55.75 ? C12 MQ7 404 C 1 
HETATM 16 C C13 MQ7 . . . S 11 4.228 -7.362 33.874 1 52.93 ? C13 MQ7 404 C 1 
HETATM 17 C C14 MQ7 . . . S 11 4.197 -5.945 33.354 1 55.69 ? C14 MQ7 404 C 1 
HETATM 18 C C15 MQ7 . . . S 11 5.482 -7.867 34.612 1 52.81 ? C15 MQ7 404 C 1 
HETATM 19 C C16 MQ7 . . . S 11 5.62 -7.084 35.945 1 58.43 ? C16 MQ7 404 C 1 
HETATM 20 C C17 MQ7 . . . S 11 4.261 -7.125 36.694 1 58.43 ? C17 MQ7 404 C 1 
HETATM 21 C C18 MQ7 . . . S 11 4.198 -7.369 38.056 1 52.76 ? C18 MQ7 404 C 1 
HETATM 22 C C19 MQ7 . . . S 11 5.467 -7.598 38.849 1 54.58 ? C19 MQ7 404 C 1 
HETATM 23 C C20 MQ7 . . . S 11 2.813 -7.405 38.78 1 52.35 ? C20 MQ7 404 C 1 
HETATM 24 C C21 MQ7 . . . S 11 2.791 -6.318 39.887 1 48.41 ? C21 MQ7 404 C 1 
HETATM 25 C C22 MQ7 . . . S 11 2.508 -4.927 39.251 1 43.04 ? C22 MQ7 404 C 1 
HETATM 26 C C23 MQ7 . . . S 11 2.897 -3.793 39.924 1 44.84 ? C23 MQ7 404 C 1 
HETATM 27 C C24 MQ7 . . . S 11 3.586 -3.921 41.251 1 50.67 ? C24 MQ7 404 C 1 
HETATM 28 C C25 MQ7 . . . S 11 2.632 -2.392 39.325 1 47.03 ? C25 MQ7 404 C 1 
HETATM 29 C C26 MQ7 . . . S 11 1.605 -1.656 40.202 1 47.13 ? C26 MQ7 404 C 1 
HETATM 30 C C27 MQ7 . . . S 11 1.025 -0.442 39.43 1 49.56 ? C27 MQ7 404 C 1 
HETATM 31 C C28 MQ7 . . . S 11 -0.284 -0.047 39.631 1 53.01 ? C28 MQ7 404 C 1 
HETATM 32 C C29 MQ7 . . . S 11 -1.178 -0.793 40.599 1 48.32 ? C29 MQ7 404 C 1 
HETATM 33 C C30 MQ7 . . . S 11 -0.834 1.162 38.858 1 62.68 ? C30 MQ7 404 C 1 
HETATM 34 C C31 MQ7 . . . S 11 -0.756 2.422 39.736 1 69.81 ? C31 MQ7 404 C 1 
HETATM 35 C C32 MQ7 . . . S 11 -1.175 3.641 38.892 1 69.56 ? C32 MQ7 404 C 1 
HETATM 36 C C33 MQ7 . . . S 11 -2.272 4.399 39.249 1 67.43 ? C33 MQ7 404 C 1 
HETATM 37 C C34 MQ7 . . . S 11 -3.077 4.057 40.476 1 68.23 ? C34 MQ7 404 C 1 
HETATM 38 C C35 MQ7 . . . S 11 -2.671 5.6 38.386 1 63.49 ? C35 MQ7 404 C 1 
HETATM 39 C C36 MQ7 . . . S 11 -3.683 5.165 37.311 1 64.66 ? C36 MQ7 404 C 1 
HETATM 40 C C37 MQ7 . . . S 11 -4.038 6.413 36.487 1 70.5 ? C37 MQ7 404 C 1 
HETATM 41 C C38 MQ7 . . . S 11 -5.309 6.68 36.078 1 70.92 ? C38 MQ7 404 C 1 
HETATM 42 C C39 MQ7 . . . S 11 -6.43 5.732 36.413 1 70.31 ? C39 MQ7 404 C 1 
HETATM 43 C C40 MQ7 . . . S 11 -5.592 7.954 35.269 1 70.52 ? C40 MQ7 404 C 1 
HETATM 44 C C41 MQ7 . . . S 11 -5.353 9.195 36.141 1 69.98 ? C41 MQ7 404 C 1 
HETATM 45 C C42 MQ7 . . . S 11 -3.874 9.601 36.094 1 71.71 ? C42 MQ7 404 C 1 
HETATM 46 C C43 MQ7 . . . S 11 -3.279 10.247 37.14 1 70.47 ? C43 MQ7 404 C 1 
HETATM 47 C C44 MQ7 . . . S 11 -1.821 10.623 37.059 1 63.86 ? C44 MQ7 404 C 1 
HETATM 48 C C45 MQ7 . . . S 11 -4.073 10.595 38.382 1 72.34 ? C45 MQ7 404 C 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           238 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           48 
#