data_2QVD # _model_server_result.job_id 0H6LBcQ8bQg_vr0SFMiPSg _model_server_result.datetime_utc '2024-10-14 12:19:49' _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 2qvd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1811}' # _entry.id 2QVD # _exptl.entry_id 2QVD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 336.361 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description BERBERINE _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 2QVD _cell.length_a 53.311 _cell.length_b 53.311 _cell.length_c 48.379 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2QVD _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _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 disulf ? disulf1 A SG CYS 26 A CYS 27 1_555 A SG CYS 115 A CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf2 A SG CYS 28 A CYS 29 1_555 A SG CYS 44 A CYS 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 A SG CYS 43 A CYS 44 1_555 A SG CYS 95 A CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 49 A CYS 50 1_555 A SG CYS 121 A CYS 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.574 ? disulf ? disulf5 A SG CYS 50 A CYS 51 1_555 A SG CYS 88 A CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf6 A SG CYS 57 A CYS 61 1_555 A SG CYS 81 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.667 ? disulf ? disulf7 A SG CYS 75 A CYS 84 1_555 A SG CYS 86 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? # _chem_comp.formula 'C20 H18 N O4 1' _chem_comp.formula_weight 336.361 _chem_comp.id BER _chem_comp.mon_nstd_flag . _chem_comp.name BERBERINE _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 C2 BER sing 70 n y C1 N1 BER doub 71 n y C1 C3 BER sing 72 n y C2 C4 BER doub 73 n y C2 C5 BER sing 74 n y N1 C6 BER sing 75 n y N1 C7 BER sing 76 n n C3 C8 BER doub 77 n y C3 H31 BER sing 78 n n C4 C9 BER sing 79 n y C4 C10 BER sing 80 n n C5 C11 BER doub 81 n y C5 H51 BER sing 82 n n C6 C12 BER doub 83 n y C6 H61 BER sing 84 n n C7 C10 BER sing 85 n n C7 H71 BER sing 86 n n C7 H72 BER sing 87 n n C8 C12 BER sing 88 n y C8 C13 BER sing 89 n y C9 C14 BER doub 90 n y C9 H91 BER sing 91 n n C10 H101 BER sing 92 n n C10 H102 BER sing 93 n n C11 C14 BER sing 94 n y C11 O1 BER sing 95 n n C12 C15 BER sing 96 n y C13 C16 BER doub 97 n y C13 H131 BER sing 98 n n C14 O2 BER sing 99 n n O1 C17 BER sing 100 n n C15 C18 BER doub 101 n y C15 O3 BER sing 102 n n C16 C18 BER sing 103 n y C16 H161 BER sing 104 n n O2 C17 BER sing 105 n n C17 H171 BER sing 106 n n C17 H172 BER sing 107 n n C18 O4 BER sing 108 n n O3 C19 BER sing 109 n n O4 C20 BER sing 110 n n C19 H191 BER sing 111 n n C19 H192 BER sing 112 n n C19 H193 BER sing 113 n n C20 H201 BER sing 114 n n C20 H202 BER sing 115 n n C20 H203 BER sing 116 n n # _atom_sites.entry_id 2QVD _atom_sites.fract_transf_matrix[1][1] 0.018758 _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] 0.018758 _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] 0.02067 _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 BER A 1 1811 1811 BER BER . C 3 HOH A 1 1812 1 HOH HOH . C 3 HOH A 2 1813 2 HOH HOH . C 3 HOH A 3 1814 3 HOH HOH . C 3 HOH A 4 1815 4 HOH HOH . C 3 HOH A 5 1816 5 HOH HOH . C 3 HOH A 6 1817 6 HOH HOH . C 3 HOH A 7 1818 7 HOH HOH . C 3 HOH A 8 1819 8 HOH HOH . C 3 HOH A 9 1820 9 HOH HOH . C 3 HOH A 10 1821 10 HOH HOH . C 3 HOH A 11 1822 11 HOH HOH . C 3 HOH A 12 1823 12 HOH HOH . C 3 HOH A 13 1824 13 HOH HOH . C 3 HOH A 14 1825 14 HOH HOH . C 3 HOH A 15 1826 15 HOH HOH . C 3 HOH A 16 1827 16 HOH HOH . C 3 HOH A 17 1828 17 HOH HOH . C 3 HOH A 18 1829 18 HOH HOH . C 3 HOH A 19 1830 19 HOH HOH . C 3 HOH A 20 1831 20 HOH HOH . C 3 HOH A 21 1832 21 HOH HOH . C 3 HOH A 22 1833 22 HOH HOH . C 3 HOH A 23 1834 23 HOH HOH . C 3 HOH A 24 1835 24 HOH HOH . C 3 HOH A 25 1836 25 HOH HOH . C 3 HOH A 26 1837 26 HOH HOH . C 3 HOH A 27 1838 27 HOH HOH . C 3 HOH A 28 1839 28 HOH HOH . C 3 HOH A 29 1840 29 HOH HOH . C 3 HOH A 30 1841 30 HOH HOH . C 3 HOH A 31 1842 31 HOH HOH . C 3 HOH A 32 1843 32 HOH HOH . C 3 HOH A 33 1844 33 HOH HOH . C 3 HOH A 34 1845 34 HOH HOH . C 3 HOH A 35 1846 35 HOH HOH . C 3 HOH A 36 1847 36 HOH HOH . C 3 HOH A 37 1848 37 HOH HOH . C 3 HOH A 38 1849 38 HOH HOH . C 3 HOH A 39 1850 39 HOH HOH . C 3 HOH A 40 1851 40 HOH HOH . C 3 HOH A 41 1852 41 HOH HOH . C 3 HOH A 42 1853 42 HOH HOH . C 3 HOH A 43 1854 43 HOH HOH . C 3 HOH A 44 1855 44 HOH HOH . C 3 HOH A 45 1856 45 HOH HOH . C 3 HOH A 46 1857 46 HOH HOH . C 3 HOH A 47 1858 47 HOH HOH . C 3 HOH A 48 1859 48 HOH HOH . C 3 HOH A 49 1860 49 HOH HOH . C 3 HOH A 50 1861 50 HOH HOH . C 3 HOH A 51 1862 51 HOH HOH . C 3 HOH A 52 1863 52 HOH HOH . C 3 HOH A 53 1864 53 HOH HOH . C 3 HOH A 54 1865 54 HOH HOH . C 3 HOH A 55 1866 55 HOH HOH . C 3 HOH A 56 1867 56 HOH HOH . C 3 HOH A 57 1868 57 HOH HOH . C 3 HOH A 58 1869 58 HOH HOH . C 3 HOH A 59 1870 59 HOH HOH . C 3 HOH A 60 1871 60 HOH HOH . C 3 HOH A 61 1872 61 HOH HOH . C 3 HOH A 62 1873 62 HOH HOH . C 3 HOH A 63 1874 63 HOH HOH . C 3 HOH A 64 1875 64 HOH HOH . C 3 HOH A 65 1876 65 HOH HOH . C 3 HOH A 66 1877 66 HOH HOH . C 3 HOH A 67 1878 67 HOH HOH . C 3 HOH A 68 1879 68 HOH HOH . C 3 HOH A 69 1880 69 HOH HOH . C 3 HOH A 70 1881 70 HOH HOH . C 3 HOH A 71 1882 71 HOH HOH . C 3 HOH A 72 1883 72 HOH HOH . C 3 HOH A 73 1884 73 HOH HOH . C 3 HOH A 74 1885 74 HOH HOH . C 3 HOH A 75 1886 75 HOH HOH . C 3 HOH A 76 1887 76 HOH HOH . C 3 HOH A 77 1888 77 HOH HOH . C 3 HOH A 78 1889 78 HOH HOH . C 3 HOH A 79 1890 79 HOH HOH . C 3 HOH A 80 1891 80 HOH HOH . C 3 HOH A 81 1892 81 HOH HOH . C 3 HOH A 82 1893 82 HOH HOH . C 3 HOH A 83 1894 83 HOH HOH . C 3 HOH A 84 1895 84 HOH HOH . C 3 HOH A 85 1896 85 HOH HOH . C 3 HOH A 86 1897 86 HOH HOH . C 3 HOH A 87 1898 87 HOH HOH . C 3 HOH A 88 1899 88 HOH HOH . C 3 HOH A 89 1900 89 HOH HOH . C 3 HOH A 90 1901 90 HOH HOH . C 3 HOH A 91 1902 91 HOH HOH . C 3 HOH A 92 1903 92 HOH HOH . C 3 HOH A 93 1904 93 HOH HOH . C 3 HOH A 94 1905 94 HOH HOH . C 3 HOH A 95 1906 95 HOH HOH . C 3 HOH A 96 1907 96 HOH HOH . C 3 HOH A 97 1908 97 HOH HOH . C 3 HOH A 98 1909 98 HOH HOH . C 3 HOH A 99 1910 99 HOH HOH . C 3 HOH A 100 1911 100 HOH HOH . C 3 HOH A 101 1912 101 HOH HOH . C 3 HOH A 102 1913 102 HOH HOH . C 3 HOH A 103 1914 103 HOH HOH . C 3 HOH A 104 1915 104 HOH HOH . C 3 HOH A 105 1916 105 HOH HOH . C 3 HOH A 106 1917 106 HOH HOH . C 3 HOH A 107 1918 107 HOH HOH . C 3 HOH A 108 1919 108 HOH HOH . C 3 HOH A 109 1920 109 HOH HOH . C 3 HOH A 110 1921 110 HOH HOH . C 3 HOH A 111 1922 111 HOH HOH . C 3 HOH A 112 1923 112 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 BER . . . B 2 21.745 47.406 -7.454 1 61.95 ? C1 BER 1811 A 1 HETATM 2 C C2 BER . . . B 2 22.425 47.448 -6.128 1 61.88 ? C2 BER 1811 A 1 HETATM 3 N N1 BER . . . B 2 20.549 48.023 -7.61 1 61.85 ? N1 BER 1811 A 1 HETATM 4 C C3 BER . . . B 2 22.412 46.672 -8.562 1 61.62 ? C3 BER 1811 A 1 HETATM 5 C C4 BER . . . B 2 21.744 48.184 -5.022 1 61.03 ? C4 BER 1811 A 1 HETATM 6 C C5 BER . . . B 2 23.657 46.815 -5.939 1 62.56 ? C5 BER 1811 A 1 HETATM 7 C C6 BER . . . B 2 19.88 48.008 -8.81 1 61.64 ? C6 BER 1811 A 1 HETATM 8 C C7 BER . . . B 2 19.965 48.671 -6.587 1 60.98 ? C7 BER 1811 A 1 HETATM 9 C C8 BER . . . B 2 21.743 46.624 -9.872 1 61.23 ? C8 BER 1811 A 1 HETATM 10 C C9 BER . . . B 2 22.311 48.281 -3.755 1 60.71 ? C9 BER 1811 A 1 HETATM 11 C C10 BER . . . B 2 20.522 48.771 -5.308 1 62.21 ? C10 BER 1811 A 1 HETATM 12 C C11 BER . . . B 2 24.202 46.926 -4.67 1 62.67 ? C11 BER 1811 A 1 HETATM 13 C C12 BER . . . B 2 20.438 47.313 -9.993 1 62 ? C12 BER 1811 A 1 HETATM 14 C C13 BER . . . B 2 22.309 45.954 -10.954 1 61.96 ? C13 BER 1811 A 1 HETATM 15 C C14 BER . . . B 2 23.537 47.648 -3.597 1 62 ? C14 BER 1811 A 1 HETATM 16 O O1 BER . . . B 2 25.42 46.417 -4.122 1 63.04 ? O1 BER 1811 A 1 HETATM 17 C C15 BER . . . B 2 19.753 47.275 -11.308 1 62.91 ? C15 BER 1811 A 1 HETATM 18 C C16 BER . . . B 2 21.671 45.903 -12.194 1 62.03 ? C16 BER 1811 A 1 HETATM 19 O O2 BER . . . B 2 24.397 47.537 -2.466 1 62.45 ? O2 BER 1811 A 1 HETATM 20 C C17 BER . . . B 2 25.531 46.793 -2.784 1 62.14 ? C17 BER 1811 A 1 HETATM 21 C C18 BER . . . B 2 20.439 46.53 -12.401 1 63.45 ? C18 BER 1811 A 1 HETATM 22 O O3 BER . . . B 2 18.528 47.87 -11.525 1 64.77 ? O3 BER 1811 A 1 HETATM 23 O O4 BER . . . B 2 19.854 46.464 -13.637 1 64.47 ? O4 BER 1811 A 1 HETATM 24 C C19 BER . . . B 2 18.364 49.292 -11.636 1 64.9 ? C19 BER 1811 A 1 HETATM 25 C C20 BER . . . B 2 19.636 45.193 -14.253 1 65.75 ? C20 BER 1811 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #