data_5M7J
#
_model_server_result.job_id            AjzncCd8crTqnMG720yofg 
_model_server_result.datetime_utc      '2024-11-23 15:54:28' 
_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          5m7j 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":403}' 
#
_entry.id    5M7J 
#
_exptl.entry_id    5M7J 
_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            5M7J 
_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                 5M7J 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
metalc ? metalc1 A NE2 HIS 111 A HIS 91 1_555 E FE HEC . A HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? 
metalc ? metalc2 A NE2 HIS 144 A HIS 124 1_555 H FE HEC . A HEC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc3 A NE2 HIS 156 A HIS 136 1_555 F FE HEC . A HEC 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? 
metalc ? metalc4 A NE2 HIS 268 A HIS 248 1_555 G FE HEC . A HEC 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? 
metalc ? metalc5 A NE2 HIS 329 A HIS 309 1_555 H FE HEC . A HEC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc6 B NE2 HIS 191 B HIS 190 1_555 P FE FE2 . B FE2 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? 
metalc ? metalc7 B NE2 HIS 231 B HIS 230 1_555 P FE FE2 . B FE2 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? 
metalc ? metalc8 P FE FE2 . B FE2 307 1_555 C NE2 HIS 218 C HIS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? 
metalc ? metalc9 P FE FE2 . B FE2 307 1_555 C OE1 GLU 233 C GLU 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? 
metalc ? metalc10 P FE FE2 . B FE2 307 1_555 C OE2 GLU 233 C GLU 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? 
metalc ? metalc11 P FE FE2 . B FE2 307 1_555 C NE2 HIS 265 C HIS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? 
#
_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                     5M7J 
_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 10 FE2 B 1 307 1326 FE2 FE2 . 
Q 7 BCL C 1 401 1324 BCL BCL . 
R 8 BPB C 1 402 1325 BPB BPB . 
S 11 MQ7 C 1 403 1327 MQ7 MQ7 . 
T 12 NS5 C 1 404 1328 NS5 NS5 . 
U 13 OTP C 1 405 1329 OTP OTP . 
V 9 MPG C 1 406 1330 MPG MPG . 
W 14 PO4 C 1 407 1331 PO4 PO4 . 
X 14 PO4 C 1 408 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 0.871 -10.616 30.38 1 53.94 ? C1 MQ7 403 C 1 
HETATM 2 O O1 MQ7 . . . S 11 0.315 -11.697 30.372 1 51.66 ? O1 MQ7 403 C 1 
HETATM 3 C C2 MQ7 . . . S 11 1.021 -9.856 31.659 1 56.14 ? C2 MQ7 403 C 1 
HETATM 4 C C2M MQ7 . . . S 11 0.481 -10.433 32.944 1 53.57 ? C2M MQ7 403 C 1 
HETATM 5 C C3 MQ7 . . . S 11 1.699 -8.543 31.663 1 58.9 ? C3 MQ7 403 C 1 
HETATM 6 C C4 MQ7 . . . S 11 2.23 -7.98 30.385 1 66.52 ? C4 MQ7 403 C 1 
HETATM 7 O O4 MQ7 . . . S 11 2.791 -6.898 30.373 1 60.6 ? O4 MQ7 403 C 1 
HETATM 8 C C5 MQ7 . . . S 11 2.069 -8.776 29.06 1 63.2 ? C5 MQ7 403 C 1 
HETATM 9 C C6 MQ7 . . . S 11 2.566 -8.248 27.868 1 60.99 ? C6 MQ7 403 C 1 
HETATM 10 C C7 MQ7 . . . S 11 2.425 -8.96 26.675 1 62.91 ? C7 MQ7 403 C 1 
HETATM 11 C C8 MQ7 . . . S 11 1.782 -10.209 26.673 1 64.6 ? C8 MQ7 403 C 1 
HETATM 12 C C9 MQ7 . . . S 11 1.281 -10.74 27.864 1 62.07 ? C9 MQ7 403 C 1 
HETATM 13 C C10 MQ7 . . . S 11 1.423 -10.029 29.057 1 60.27 ? C10 MQ7 403 C 1 
HETATM 14 C C11 MQ7 . . . S 11 1.855 -7.759 32.986 1 53.36 ? C11 MQ7 403 C 1 
HETATM 15 C C12 MQ7 . . . S 11 3.109 -8.239 33.713 1 51.46 ? C12 MQ7 403 C 1 
HETATM 16 C C13 MQ7 . . . S 11 4.219 -7.421 33.857 1 44.84 ? C13 MQ7 403 C 1 
HETATM 17 C C14 MQ7 . . . S 11 4.217 -6.022 33.292 1 47.88 ? C14 MQ7 403 C 1 
HETATM 18 C C15 MQ7 . . . S 11 5.468 -7.936 34.6 1 39.1 ? C15 MQ7 403 C 1 
HETATM 19 C C16 MQ7 . . . S 11 5.599 -7.179 35.948 1 53.17 ? C16 MQ7 403 C 1 
HETATM 20 C C17 MQ7 . . . S 11 4.235 -7.206 36.69 1 50.56 ? C17 MQ7 403 C 1 
HETATM 21 C C18 MQ7 . . . S 11 4.173 -7.377 38.063 1 45.35 ? C18 MQ7 403 C 1 
HETATM 22 C C19 MQ7 . . . S 11 5.448 -7.542 38.865 1 45.07 ? C19 MQ7 403 C 1 
HETATM 23 C C20 MQ7 . . . S 11 2.786 -7.404 38.785 1 50.52 ? C20 MQ7 403 C 1 
HETATM 24 C C21 MQ7 . . . S 11 2.767 -6.346 39.919 1 41.92 ? C21 MQ7 403 C 1 
HETATM 25 C C22 MQ7 . . . S 11 2.475 -4.946 39.31 1 27.07 ? C22 MQ7 403 C 1 
HETATM 26 C C23 MQ7 . . . S 11 2.918 -3.829 39.975 1 27.52 ? C23 MQ7 403 C 1 
HETATM 27 C C24 MQ7 . . . S 11 3.67 -3.987 41.265 1 42.99 ? C24 MQ7 403 C 1 
HETATM 28 C C25 MQ7 . . . S 11 2.648 -2.42 39.402 1 29.49 ? C25 MQ7 403 C 1 
HETATM 29 C C26 MQ7 . . . S 11 1.541 -1.743 40.227 1 33.45 ? C26 MQ7 403 C 1 
HETATM 30 C C27 MQ7 . . . S 11 0.992 -0.517 39.45 1 40.63 ? C27 MQ7 403 C 1 
HETATM 31 C C28 MQ7 . . . S 11 -0.309 -0.092 39.64 1 45.36 ? C28 MQ7 403 C 1 
HETATM 32 C C29 MQ7 . . . S 11 -1.223 -0.818 40.604 1 37.02 ? C29 MQ7 403 C 1 
HETATM 33 C C30 MQ7 . . . S 11 -0.83 1.127 38.86 1 64.48 ? C30 MQ7 403 C 1 
HETATM 34 C C31 MQ7 . . . S 11 -0.786 2.375 39.755 1 68.72 ? C31 MQ7 403 C 1 
HETATM 35 C C32 MQ7 . . . S 11 -1.186 3.603 38.915 1 64.07 ? C32 MQ7 403 C 1 
HETATM 36 C C33 MQ7 . . . S 11 -2.315 4.33 39.235 1 59.99 ? C33 MQ7 403 C 1 
HETATM 37 C C34 MQ7 . . . S 11 -3.168 3.936 40.413 1 64.35 ? C34 MQ7 403 C 1 
HETATM 38 C C35 MQ7 . . . S 11 -2.7 5.545 38.386 1 53.43 ? C35 MQ7 403 C 1 
HETATM 39 C C36 MQ7 . . . S 11 -3.674 5.117 37.274 1 59.07 ? C36 MQ7 403 C 1 
HETATM 40 C C37 MQ7 . . . S 11 -4.032 6.374 36.464 1 67.75 ? C37 MQ7 403 C 1 
HETATM 41 C C38 MQ7 . . . S 11 -5.308 6.649 36.075 1 69.36 ? C38 MQ7 403 C 1 
HETATM 42 C C39 MQ7 . . . S 11 -6.429 5.704 36.422 1 65.45 ? C39 MQ7 403 C 1 
HETATM 43 C C40 MQ7 . . . S 11 -5.599 7.928 35.277 1 65.52 ? C40 MQ7 403 C 1 
HETATM 44 C C41 MQ7 . . . S 11 -5.372 9.168 36.152 1 55.56 ? C41 MQ7 403 C 1 
HETATM 45 C C42 MQ7 . . . S 11 -3.901 9.594 36.084 1 60.24 ? C42 MQ7 403 C 1 
HETATM 46 C C43 MQ7 . . . S 11 -3.3 10.234 37.13 1 54.17 ? C43 MQ7 403 C 1 
HETATM 47 C C44 MQ7 . . . S 11 -1.849 10.633 37.035 1 40.52 ? C44 MQ7 403 C 1 
HETATM 48 C C45 MQ7 . . . S 11 -4.083 10.548 38.387 1 60 ? C45 MQ7 403 C 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          15 
_model_server_stats.element_count           48 
#