data_5MG2 # _model_server_result.job_id SoK83w4GQUybdnuvpJBMiQ _model_server_result.datetime_utc '2024-12-21 12:12:10' _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 5mg2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1704}' # _entry.id 5MG2 # _exptl.entry_id 5MG2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 429.468 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-(3-oxidanylpropyl)-2-(1,3,6-trimethyl-2-oxidanylidene-benzimidazol-5-yl)benzo[de]isoquinoline-1,3-dione _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 120 _cell.entry_id 5MG2 _cell.length_a 64.739 _cell.length_b 64.739 _cell.length_c 101.082 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MG2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C25 H23 N3 O4' _chem_comp.formula_weight 429.468 _chem_comp.id 7M8 _chem_comp.mon_nstd_flag . _chem_comp.name 6-(3-oxidanylpropyl)-2-(1,3,6-trimethyl-2-oxidanylidene-benzimidazol-5-yl)benzo[de]isoquinoline-1,3-dione _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 O1 C20 7M8 doub 1 n n C22 N1 7M8 sing 2 n n C20 N1 7M8 sing 3 n n C20 N2 7M8 sing 4 n n N1 C18 7M8 sing 5 n n N2 C21 7M8 sing 6 n n N2 C17 7M8 sing 7 n n C18 C17 7M8 doub 8 n y C18 C19 7M8 sing 9 n y C17 C16 7M8 sing 10 n y C19 C14 7M8 doub 11 n y O3 C24 7M8 doub 12 n n C16 C15 7M8 doub 13 n y C14 C15 7M8 sing 14 n y C14 N 7M8 sing 15 n n C24 N 7M8 sing 16 n n C24 C3 7M8 sing 17 n n C2 C3 7M8 doub 18 n y C2 C1 7M8 sing 19 n y C15 C23 7M8 sing 20 n n N C13 7M8 sing 21 n n C3 C4 7M8 sing 22 n y C1 C 7M8 doub 23 n y C4 C5 7M8 doub 24 n y C4 C10 7M8 sing 25 n y C C5 7M8 sing 26 n y C13 C10 7M8 sing 27 n n C13 O2 7M8 doub 28 n n C5 C6 7M8 sing 29 n y C10 C11 7M8 doub 30 n y C11 C12 7M8 sing 31 n y C6 C12 7M8 doub 32 n y C6 C7 7M8 sing 33 n n C7 C8 7M8 sing 34 n n C8 C9 7M8 sing 35 n n C9 O 7M8 sing 36 n n C1 H1 7M8 sing 37 n n C2 H2 7M8 sing 38 n n C8 H3 7M8 sing 39 n n C8 H4 7M8 sing 40 n n C9 H5 7M8 sing 41 n n C9 H6 7M8 sing 42 n n C11 H7 7M8 sing 43 n n C12 H8 7M8 sing 44 n n C16 H9 7M8 sing 45 n n C19 H10 7M8 sing 46 n n C21 H11 7M8 sing 47 n n C21 H12 7M8 sing 48 n n C21 H13 7M8 sing 49 n n C7 H14 7M8 sing 50 n n C7 H15 7M8 sing 51 n n O H16 7M8 sing 52 n n C H17 7M8 sing 53 n n C22 H18 7M8 sing 54 n n C22 H19 7M8 sing 55 n n C22 H20 7M8 sing 56 n n C23 H21 7M8 sing 57 n n C23 H22 7M8 sing 58 n n C23 H23 7M8 sing 59 n n # _atom_sites.entry_id 5MG2 _atom_sites.fract_transf_matrix[1][1] 0.015447 _atom_sites.fract_transf_matrix[1][2] 0.008918 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017836 _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] 0.009893 _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 B 2 EDO A 1 1701 1 EDO EDO . C 2 EDO A 1 1702 2 EDO EDO . D 2 EDO A 1 1703 3 EDO EDO . E 3 7M8 A 1 1704 1 7M8 BAY . F 4 HOH A 1 1801 61 HOH HOH . F 4 HOH A 2 1802 13 HOH HOH . F 4 HOH A 3 1803 60 HOH HOH . F 4 HOH A 4 1804 36 HOH HOH . F 4 HOH A 5 1805 26 HOH HOH . F 4 HOH A 6 1806 4 HOH HOH . F 4 HOH A 7 1807 47 HOH HOH . F 4 HOH A 8 1808 63 HOH HOH . F 4 HOH A 9 1809 30 HOH HOH . F 4 HOH A 10 1810 8 HOH HOH . F 4 HOH A 11 1811 15 HOH HOH . F 4 HOH A 12 1812 54 HOH HOH . F 4 HOH A 13 1813 40 HOH HOH . F 4 HOH A 14 1814 28 HOH HOH . F 4 HOH A 15 1815 16 HOH HOH . F 4 HOH A 16 1816 62 HOH HOH . F 4 HOH A 17 1817 39 HOH HOH . F 4 HOH A 18 1818 27 HOH HOH . F 4 HOH A 19 1819 35 HOH HOH . F 4 HOH A 20 1820 64 HOH HOH . F 4 HOH A 21 1821 59 HOH HOH . F 4 HOH A 22 1822 12 HOH HOH . F 4 HOH A 23 1823 41 HOH HOH . F 4 HOH A 24 1824 20 HOH HOH . F 4 HOH A 25 1825 70 HOH HOH . F 4 HOH A 26 1826 10 HOH HOH . F 4 HOH A 27 1827 46 HOH HOH . F 4 HOH A 28 1828 2 HOH HOH . F 4 HOH A 29 1829 56 HOH HOH . F 4 HOH A 30 1830 22 HOH HOH . F 4 HOH A 31 1831 43 HOH HOH . F 4 HOH A 32 1832 49 HOH HOH . F 4 HOH A 33 1833 42 HOH HOH . F 4 HOH A 34 1834 84 HOH HOH . F 4 HOH A 35 1835 66 HOH HOH . F 4 HOH A 36 1836 9 HOH HOH . F 4 HOH A 37 1837 23 HOH HOH . F 4 HOH A 38 1838 1 HOH HOH . F 4 HOH A 39 1839 65 HOH HOH . F 4 HOH A 40 1840 3 HOH HOH . F 4 HOH A 41 1841 76 HOH HOH . F 4 HOH A 42 1842 24 HOH HOH . F 4 HOH A 43 1843 32 HOH HOH . F 4 HOH A 44 1844 57 HOH HOH . F 4 HOH A 45 1845 14 HOH HOH . F 4 HOH A 46 1846 53 HOH HOH . F 4 HOH A 47 1847 37 HOH HOH . F 4 HOH A 48 1848 48 HOH HOH . F 4 HOH A 49 1849 25 HOH HOH . F 4 HOH A 50 1850 33 HOH HOH . F 4 HOH A 51 1851 50 HOH HOH . F 4 HOH A 52 1852 74 HOH HOH . F 4 HOH A 53 1853 45 HOH HOH . F 4 HOH A 54 1854 71 HOH HOH . F 4 HOH A 55 1855 18 HOH HOH . F 4 HOH A 56 1856 21 HOH HOH . F 4 HOH A 57 1857 58 HOH HOH . F 4 HOH A 58 1858 73 HOH HOH . F 4 HOH A 59 1859 5 HOH HOH . F 4 HOH A 60 1860 19 HOH HOH . F 4 HOH A 61 1861 67 HOH HOH . F 4 HOH A 62 1862 7 HOH HOH . F 4 HOH A 63 1863 17 HOH HOH . F 4 HOH A 64 1864 80 HOH HOH . F 4 HOH A 65 1865 29 HOH HOH . F 4 HOH A 66 1866 38 HOH HOH . F 4 HOH A 67 1867 6 HOH HOH . F 4 HOH A 68 1868 11 HOH HOH . F 4 HOH A 69 1869 72 HOH HOH . F 4 HOH A 70 1870 34 HOH HOH . F 4 HOH A 71 1871 77 HOH HOH . F 4 HOH A 72 1872 51 HOH HOH . F 4 HOH A 73 1873 82 HOH HOH . F 4 HOH A 74 1874 81 HOH HOH . F 4 HOH A 75 1875 85 HOH HOH . F 4 HOH A 76 1876 44 HOH HOH . F 4 HOH A 77 1877 78 HOH HOH . F 4 HOH A 78 1878 55 HOH HOH . F 4 HOH A 79 1879 52 HOH HOH . F 4 HOH A 80 1880 31 HOH HOH . F 4 HOH A 81 1881 75 HOH HOH . F 4 HOH A 82 1882 69 HOH HOH . F 4 HOH A 83 1883 68 HOH HOH . F 4 HOH A 84 1884 83 HOH HOH . F 4 HOH A 85 1885 79 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 7M8 . A . E 3 23.014 68.598 17.401 0.5 31.18 ? C1 7M8 1704 A 1 HETATM 2 C C1 7M8 . B . E 3 19.31 67.539 20.249 0.5 28.55 ? C1 7M8 1704 A 1 HETATM 3 C C2 7M8 . A . E 3 22.31 69.676 16.888 0.5 29.04 ? C2 7M8 1704 A 1 HETATM 4 C C2 7M8 . B . E 3 18.615 68.645 19.793 0.5 28.47 ? C2 7M8 1704 A 1 HETATM 5 C C3 7M8 . A . E 3 21.044 69.958 17.345 0.5 29.53 ? C3 7M8 1704 A 1 HETATM 6 C C3 7M8 . B . E 3 19.18 69.47 18.847 0.5 28.56 ? C3 7M8 1704 A 1 HETATM 7 C C4 7M8 . A . E 3 20.453 69.151 18.347 0.5 29.89 ? C4 7M8 1704 A 1 HETATM 8 C C4 7M8 . B . E 3 20.465 69.182 18.324 0.5 29.21 ? C4 7M8 1704 A 1 HETATM 9 C C8 7M8 . A . E 3 20.341 65.082 21.279 0.5 42 ? C8 7M8 1704 A 1 HETATM 10 C C8 7M8 . B . E 3 24.739 66.58 18.241 0.5 38.44 ? C8 7M8 1704 A 1 HETATM 11 C C9 7M8 . A . E 3 20.967 63.731 21.494 0.5 40.68 ? C9 7M8 1704 A 1 HETATM 12 C C9 7M8 . B . E 3 25.171 65.191 18.054 0.5 40.49 ? C9 7M8 1704 A 1 HETATM 13 C C10 7M8 . A . E 3 19.17 69.452 18.86 0.5 29.49 ? C10 7M8 1704 A 1 HETATM 14 C C10 7M8 . B . E 3 21.04 69.994 17.321 0.5 29.11 ? C10 7M8 1704 A 1 HETATM 15 C C11 7M8 . A . E 3 18.594 68.63 19.801 0.5 29.82 ? C11 7M8 1704 A 1 HETATM 16 C C11 7M8 . B . E 3 22.305 69.722 16.858 0.5 28.96 ? C11 7M8 1704 A 1 HETATM 17 C C12 7M8 . A . E 3 19.264 67.512 20.269 0.5 31.29 ? C12 7M8 1704 A 1 HETATM 18 C C12 7M8 . B . E 3 23.032 68.654 17.359 0.5 31.25 ? C12 7M8 1704 A 1 HETATM 19 C C13 7M8 . A . E 3 18.429 70.63 18.363 0.5 27.9 ? C13 7M8 1704 A 1 HETATM 20 C C13 7M8 . B . E 3 20.282 71.134 16.765 0.5 27.94 ? C13 7M8 1704 A 1 HETATM 21 C C14 7M8 . A . E 3 18.217 72.339 16.665 0.5 29.36 ? C14 7M8 1704 A 1 HETATM 22 C C14 7M8 . B . E 3 18.196 72.354 16.666 0.5 29.26 ? C14 7M8 1704 A 1 HETATM 23 C C15 7M8 . A . E 3 18.2 73.645 17.161 0.5 28.5 ? C15 7M8 1704 A 1 HETATM 24 C C15 7M8 . B . E 3 18.18 73.66 17.16 0.5 28.48 ? C15 7M8 1704 A 1 HETATM 25 C C16 7M8 . A . E 3 17.439 74.597 16.478 0.5 28.54 ? C16 7M8 1704 A 1 HETATM 26 C C16 7M8 . B . E 3 17.421 74.612 16.474 0.5 28.46 ? C16 7M8 1704 A 1 HETATM 27 C C17 7M8 . A . E 3 16.711 74.219 15.354 0.5 28.55 ? C17 7M8 1704 A 1 HETATM 28 C C17 7M8 . B . E 3 16.695 74.232 15.35 0.5 28.54 ? C17 7M8 1704 A 1 HETATM 29 C C18 7M8 . A . E 3 16.731 72.91 14.899 0.5 29.48 ? C18 7M8 1704 A 1 HETATM 30 C C18 7M8 . B . E 3 16.713 72.921 14.898 0.5 29.41 ? C18 7M8 1704 A 1 HETATM 31 C C19 7M8 . A . E 3 17.486 71.95 15.543 0.5 27.49 ? C19 7M8 1704 A 1 HETATM 32 C C19 7M8 . B . E 3 17.465 71.963 15.545 0.5 27.56 ? C19 7M8 1704 A 1 HETATM 33 C C20 7M8 . A . E 3 15.353 74.089 13.524 0.5 29.03 ? C20 7M8 1704 A 1 HETATM 34 C C20 7M8 . B . E 3 15.342 74.099 13.518 0.5 29.01 ? C20 7M8 1704 A 1 HETATM 35 C C21 7M8 . A . E 3 15.542 76.356 14.601 0.5 29.47 ? C21 7M8 1704 A 1 HETATM 36 C C21 7M8 . B . E 3 15.533 76.369 14.589 0.5 29.39 ? C21 7M8 1704 A 1 HETATM 37 C C24 7M8 . A . E 3 20.297 71.103 16.78 0.5 28.09 ? C24 7M8 1704 A 1 HETATM 38 C C24 7M8 . B . E 3 18.427 70.644 18.357 0.5 27.56 ? C24 7M8 1704 A 1 HETATM 39 O O3 7M8 . A . E 3 20.727 71.796 15.871 0.5 32.73 ? O3 7M8 1704 A 1 HETATM 40 O O3 7M8 . B . E 3 17.378 71.021 18.86 0.5 28.46 ? O3 7M8 1704 A 1 HETATM 41 N N 7M8 . A . E 3 19.027 71.35 17.319 0.5 28.43 ? N 7M8 1704 A 1 HETATM 42 N N 7M8 . B . E 3 19.014 71.371 17.312 0.5 28.29 ? N 7M8 1704 A 1 HETATM 43 O O2 7M8 . A . E 3 17.381 71.018 18.86 0.5 28.79 ? O2 7M8 1704 A 1 HETATM 44 O O2 7M8 . B . E 3 20.701 71.832 15.855 0.5 32.35 ? O2 7M8 1704 A 1 HETATM 45 C C6 7M8 . A . E 3 20.527 67.193 19.827 0.5 35.45 ? C6 7M8 1704 A 1 HETATM 46 C C6 7M8 . B . E 3 22.506 67.82 18.318 0.5 33.04 ? C6 7M8 1704 A 1 HETATM 47 C C7 7M8 . A . E 3 21.229 65.973 20.385 0.5 38.38 ? C7 7M8 1704 A 1 HETATM 48 C C7 7M8 . B . E 3 23.334 66.667 18.843 0.5 35.67 ? C7 7M8 1704 A 1 HETATM 49 O O 7M8 . A . E 3 22.267 63.972 21.96 0.5 46.02 ? O 7M8 1704 A 1 HETATM 50 O O 7M8 . B . E 3 25.263 64.589 19.325 0.5 44.96 ? O 7M8 1704 A 1 HETATM 51 C C5 7M8 . A . E 3 21.154 68.026 18.846 0.5 30.91 ? C5 7M8 1704 A 1 HETATM 52 C C5 7M8 . B . E 3 21.188 68.068 18.811 0.5 29.51 ? C5 7M8 1704 A 1 HETATM 53 C C 7M8 . A . E 3 22.459 67.782 18.349 0.5 31.98 ? C 7M8 1704 A 1 HETATM 54 C C 7M8 . B . E 3 20.563 67.251 19.788 0.5 31.51 ? C 7M8 1704 A 1 HETATM 55 N N1 7M8 . A . E 3 15.901 72.844 13.775 0.5 29.83 ? N1 7M8 1704 A 1 HETATM 56 N N1 7M8 . B . E 3 15.886 72.854 13.773 0.5 29.73 ? N1 7M8 1704 A 1 HETATM 57 C C22 7M8 . A . E 3 15.664 71.655 12.963 0.5 31.57 ? C22 7M8 1704 A 1 HETATM 58 C C22 7M8 . B . E 3 15.652 71.664 12.963 0.5 31.64 ? C22 7M8 1704 A 1 HETATM 59 O O1 7M8 . A . E 3 14.563 74.383 12.645 0.5 31.06 ? O1 7M8 1704 A 1 HETATM 60 O O1 7M8 . B . E 3 14.554 74.392 12.636 0.5 30.97 ? O1 7M8 1704 A 1 HETATM 61 N N2 7M8 . A . E 3 15.863 74.935 14.503 0.5 28.24 ? N2 7M8 1704 A 1 HETATM 62 N N2 7M8 . B . E 3 15.851 74.947 14.495 0.5 28.27 ? N2 7M8 1704 A 1 HETATM 63 C C23 7M8 . A . E 3 18.93 74.027 18.424 0.5 28.6 ? C23 7M8 1704 A 1 HETATM 64 C C23 7M8 . B . E 3 18.911 74.044 18.422 0.5 28.64 ? C23 7M8 1704 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 64 #