data_8U2A # _model_server_result.job_id hw2XzbRKQo3NcYDh5yefng _model_server_result.datetime_utc '2024-11-24 13:45:30' _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 8u2a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1705}' # _entry.id 8U2A # _exptl.entry_id 8U2A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 351.307 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid' _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 8U2A _cell.length_a 69.482 _cell.length_b 72.331 _cell.length_c 97.347 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8U2A _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 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,D,E,F,G _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 5 _struct_asym.id F _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 OD1 ASP 54 A ASP 1296 1_555 D NA NA . A NA 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc2 A OD1 ASP 56 A ASP 1298 1_555 D NA NA . A NA 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc3 A OD1 ASP 77 A ASP 1319 1_555 D NA NA . A NA 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc4 A O TYR 78 A TYR 1320 1_555 D NA NA . A NA 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc5 D NA NA . A NA 1703 1_555 G O HOH . A HOH 1864 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc6 D NA NA . A NA 1703 1_555 G O HOH . A HOH 1876 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc7 D NA NA . A NA 1703 1_555 G O HOH . A HOH 1915 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? # _chem_comp.formula 'C13 H21 N O10' _chem_comp.formula_weight 351.307 _chem_comp.id 5N6 _chem_comp.mon_nstd_flag n _chem_comp.name '9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid' _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms '(2~{R},4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{R})-3-acetyloxy-1,2-bis(oxidanyl)propyl]-2,4-bis(oxidanyl)oxane-2-ca rboxylic acid;9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosonic acid;9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid;9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosonic acid' # 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 C3 C2 5N6 sing 1 n n C3 C4 5N6 sing 2 n n C2 C1 5N6 sing 3 n n C2 O6 5N6 sing 4 n n O1A C1 5N6 doub 5 n n C1 O1B 5N6 sing 6 n n O4 C4 5N6 sing 7 n n O6 C6 5N6 sing 8 n n C4 C5 5N6 sing 9 n n C5 C6 5N6 sing 10 n n C5 N5 5N6 sing 11 n n C6 C7 5N6 sing 12 n n C8 O8 5N6 sing 13 n n C8 C7 5N6 sing 14 n n C8 C9 5N6 sing 15 n n N5 C10 5N6 sing 16 n n C7 O7 5N6 sing 17 n n C9 O9 5N6 sing 18 n n C10 O10 5N6 doub 19 n n C10 C11 5N6 sing 20 n n O9 CAG 5N6 sing 21 n n CAG OBJ 5N6 doub 22 n n CAG CAF 5N6 sing 23 n n CAF H1 5N6 sing 24 n n CAF H2 5N6 sing 25 n n CAF H3 5N6 sing 26 n n C11 H111 5N6 sing 27 n n C11 H113 5N6 sing 28 n n C11 H112 5N6 sing 29 n n C9 H92 5N6 sing 30 n n C9 H91 5N6 sing 31 n n C8 H8 5N6 sing 32 n n C7 H7 5N6 sing 33 n n N5 HN5 5N6 sing 34 n n C5 H5 5N6 sing 35 n n C4 H4 5N6 sing 36 n n C6 H6 5N6 sing 37 n n C3 H32 5N6 sing 38 n n C3 H31 5N6 sing 39 n n O7 HO7 5N6 sing 40 n n O8 HO8 5N6 sing 41 n n O4 HO4 5N6 sing 42 n n O1B HO1B 5N6 sing 43 n n C2 O2 5N6 sing 44 n n O2 HO2 5N6 sing 45 n n # _pdbx_chem_comp_identifier.comp_id 5N6 _pdbx_chem_comp_identifier.identifier a-D-Neup5Ac9Ac _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 8U2A _atom_sites.fract_transf_matrix[1][1] 0.014392 _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] 0.013825 _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] 0.010273 _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 NO3 A 1 1701 502 NO3 NO3 . C 3 NA A 1 1702 1 NA NA . D 3 NA A 1 1703 2 NA NA . E 4 EDO A 1 1704 503 EDO EDO . F 5 5N6 A 1 1705 504 5N6 5N6 . G 6 HOH A 1 1801 105 HOH HOH . G 6 HOH A 2 1802 89 HOH HOH . G 6 HOH A 3 1803 83 HOH HOH . G 6 HOH A 4 1804 156 HOH HOH . G 6 HOH A 5 1805 98 HOH HOH . G 6 HOH A 6 1806 88 HOH HOH . G 6 HOH A 7 1807 72 HOH HOH . G 6 HOH A 8 1808 145 HOH HOH . G 6 HOH A 9 1809 87 HOH HOH . G 6 HOH A 10 1810 27 HOH HOH . G 6 HOH A 11 1811 111 HOH HOH . G 6 HOH A 12 1812 122 HOH HOH . G 6 HOH A 13 1813 36 HOH HOH . G 6 HOH A 14 1814 30 HOH HOH . G 6 HOH A 15 1815 8 HOH HOH . G 6 HOH A 16 1816 22 HOH HOH . G 6 HOH A 17 1817 58 HOH HOH . G 6 HOH A 18 1818 92 HOH HOH . G 6 HOH A 19 1819 147 HOH HOH . G 6 HOH A 20 1820 112 HOH HOH . G 6 HOH A 21 1821 150 HOH HOH . G 6 HOH A 22 1822 64 HOH HOH . G 6 HOH A 23 1823 4 HOH HOH . G 6 HOH A 24 1824 13 HOH HOH . G 6 HOH A 25 1825 65 HOH HOH . G 6 HOH A 26 1826 155 HOH HOH . G 6 HOH A 27 1827 133 HOH HOH . G 6 HOH A 28 1828 93 HOH HOH . G 6 HOH A 29 1829 14 HOH HOH . G 6 HOH A 30 1830 1 HOH HOH . G 6 HOH A 31 1831 152 HOH HOH . G 6 HOH A 32 1832 81 HOH HOH . G 6 HOH A 33 1833 62 HOH HOH . G 6 HOH A 34 1834 70 HOH HOH . G 6 HOH A 35 1835 54 HOH HOH . G 6 HOH A 36 1836 46 HOH HOH . G 6 HOH A 37 1837 106 HOH HOH . G 6 HOH A 38 1838 154 HOH HOH . G 6 HOH A 39 1839 18 HOH HOH . G 6 HOH A 40 1840 20 HOH HOH . G 6 HOH A 41 1841 96 HOH HOH . G 6 HOH A 42 1842 53 HOH HOH . G 6 HOH A 43 1843 7 HOH HOH . G 6 HOH A 44 1844 3 HOH HOH . G 6 HOH A 45 1845 23 HOH HOH . G 6 HOH A 46 1846 71 HOH HOH . G 6 HOH A 47 1847 120 HOH HOH . G 6 HOH A 48 1848 26 HOH HOH . G 6 HOH A 49 1849 100 HOH HOH . G 6 HOH A 50 1850 6 HOH HOH . G 6 HOH A 51 1851 158 HOH HOH . G 6 HOH A 52 1852 127 HOH HOH . G 6 HOH A 53 1853 143 HOH HOH . G 6 HOH A 54 1854 15 HOH HOH . G 6 HOH A 55 1855 55 HOH HOH . G 6 HOH A 56 1856 69 HOH HOH . G 6 HOH A 57 1857 16 HOH HOH . G 6 HOH A 58 1858 24 HOH HOH . G 6 HOH A 59 1859 51 HOH HOH . G 6 HOH A 60 1860 52 HOH HOH . G 6 HOH A 61 1861 128 HOH HOH . G 6 HOH A 62 1862 29 HOH HOH . G 6 HOH A 63 1863 144 HOH HOH . G 6 HOH A 64 1864 34 HOH HOH . G 6 HOH A 65 1865 9 HOH HOH . G 6 HOH A 66 1866 33 HOH HOH . G 6 HOH A 67 1867 12 HOH HOH . G 6 HOH A 68 1868 151 HOH HOH . G 6 HOH A 69 1869 35 HOH HOH . G 6 HOH A 70 1870 43 HOH HOH . G 6 HOH A 71 1871 5 HOH HOH . G 6 HOH A 72 1872 2 HOH HOH . G 6 HOH A 73 1873 113 HOH HOH . G 6 HOH A 74 1874 130 HOH HOH . G 6 HOH A 75 1875 17 HOH HOH . G 6 HOH A 76 1876 82 HOH HOH . G 6 HOH A 77 1877 60 HOH HOH . G 6 HOH A 78 1878 153 HOH HOH . G 6 HOH A 79 1879 47 HOH HOH . G 6 HOH A 80 1880 11 HOH HOH . G 6 HOH A 81 1881 19 HOH HOH . G 6 HOH A 82 1882 137 HOH HOH . G 6 HOH A 83 1883 74 HOH HOH . G 6 HOH A 84 1884 59 HOH HOH . G 6 HOH A 85 1885 99 HOH HOH . G 6 HOH A 86 1886 126 HOH HOH . G 6 HOH A 87 1887 21 HOH HOH . G 6 HOH A 88 1888 45 HOH HOH . G 6 HOH A 89 1889 146 HOH HOH . G 6 HOH A 90 1890 95 HOH HOH . G 6 HOH A 91 1891 160 HOH HOH . G 6 HOH A 92 1892 48 HOH HOH . G 6 HOH A 93 1893 118 HOH HOH . G 6 HOH A 94 1894 80 HOH HOH . G 6 HOH A 95 1895 28 HOH HOH . G 6 HOH A 96 1896 117 HOH HOH . G 6 HOH A 97 1897 135 HOH HOH . G 6 HOH A 98 1898 42 HOH HOH . G 6 HOH A 99 1899 77 HOH HOH . G 6 HOH A 100 1900 31 HOH HOH . G 6 HOH A 101 1901 79 HOH HOH . G 6 HOH A 102 1902 119 HOH HOH . G 6 HOH A 103 1903 63 HOH HOH . G 6 HOH A 104 1904 132 HOH HOH . G 6 HOH A 105 1905 38 HOH HOH . G 6 HOH A 106 1906 39 HOH HOH . G 6 HOH A 107 1907 90 HOH HOH . G 6 HOH A 108 1908 102 HOH HOH . G 6 HOH A 109 1909 44 HOH HOH . G 6 HOH A 110 1910 107 HOH HOH . G 6 HOH A 111 1911 50 HOH HOH . G 6 HOH A 112 1912 86 HOH HOH . G 6 HOH A 113 1913 78 HOH HOH . G 6 HOH A 114 1914 91 HOH HOH . G 6 HOH A 115 1915 131 HOH HOH . G 6 HOH A 116 1916 67 HOH HOH . G 6 HOH A 117 1917 148 HOH HOH . G 6 HOH A 118 1918 136 HOH HOH . G 6 HOH A 119 1919 139 HOH HOH . G 6 HOH A 120 1920 94 HOH HOH . G 6 HOH A 121 1921 56 HOH HOH . G 6 HOH A 122 1922 73 HOH HOH . G 6 HOH A 123 1923 32 HOH HOH . G 6 HOH A 124 1924 123 HOH HOH . G 6 HOH A 125 1925 37 HOH HOH . G 6 HOH A 126 1926 141 HOH HOH . G 6 HOH A 127 1927 25 HOH HOH . G 6 HOH A 128 1928 66 HOH HOH . G 6 HOH A 129 1929 103 HOH HOH . G 6 HOH A 130 1930 134 HOH HOH . G 6 HOH A 131 1931 125 HOH HOH . G 6 HOH A 132 1932 142 HOH HOH . G 6 HOH A 133 1933 57 HOH HOH . G 6 HOH A 134 1934 85 HOH HOH . G 6 HOH A 135 1935 121 HOH HOH . G 6 HOH A 136 1936 41 HOH HOH . G 6 HOH A 137 1937 108 HOH HOH . G 6 HOH A 138 1938 104 HOH HOH . G 6 HOH A 139 1939 10 HOH HOH . G 6 HOH A 140 1940 68 HOH HOH . G 6 HOH A 141 1941 124 HOH HOH . G 6 HOH A 142 1942 138 HOH HOH . G 6 HOH A 143 1943 116 HOH HOH . G 6 HOH A 144 1944 149 HOH HOH . G 6 HOH A 145 1945 157 HOH HOH . G 6 HOH A 146 1946 115 HOH HOH . G 6 HOH A 147 1947 129 HOH HOH . G 6 HOH A 148 1948 110 HOH HOH . G 6 HOH A 149 1949 76 HOH HOH . G 6 HOH A 150 1950 75 HOH HOH . G 6 HOH A 151 1951 97 HOH HOH . G 6 HOH A 152 1952 159 HOH HOH . G 6 HOH A 153 1953 49 HOH HOH . G 6 HOH A 154 1954 140 HOH HOH . G 6 HOH A 155 1955 61 HOH HOH . G 6 HOH A 156 1956 109 HOH HOH . G 6 HOH A 157 1957 101 HOH HOH . G 6 HOH A 158 1958 161 HOH HOH . G 6 HOH A 159 1959 114 HOH HOH . G 6 HOH A 160 1960 40 HOH HOH . G 6 HOH A 161 1961 84 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 CAF 5N6 . . . F 5 -10.179 -35.589 17.449 1 23.93 ? CAF 5N6 1705 A 1 HETATM 2 C CAG 5N6 . . . F 5 -9.037 -36.642 17.524 1 28.7 ? CAG 5N6 1705 A 1 HETATM 3 C C11 5N6 . . . F 5 -6.521 -34.352 21.988 1 21.45 ? C11 5N6 1705 A 1 HETATM 4 C C10 5N6 . . . F 5 -6.083 -33.04 21.358 1 29.8 ? C10 5N6 1705 A 1 HETATM 5 C C9 5N6 . . . F 5 -6.798 -37.333 17.847 1 26.73 ? C9 5N6 1705 A 1 HETATM 6 C C8 5N6 . . . F 5 -5.44 -36.691 18.102 1 25.06 ? C8 5N6 1705 A 1 HETATM 7 C C7 5N6 . . . F 5 -5.522 -35.726 19.337 1 26.56 ? C7 5N6 1705 A 1 HETATM 8 N N5 5N6 . . . F 5 -4.78 -33.029 20.698 1 23.72 ? N5 5N6 1705 A 1 HETATM 9 C C5 5N6 . . . F 5 -3.932 -34.256 20.658 1 23.92 ? C5 5N6 1705 A 1 HETATM 10 C C4 5N6 . . . F 5 -2.503 -33.825 20.621 1 24.11 ? C4 5N6 1705 A 1 HETATM 11 C C6 5N6 . . . F 5 -4.246 -35.008 19.367 1 30.5 ? C6 5N6 1705 A 1 HETATM 12 C C3 5N6 . . . F 5 -1.585 -34.973 20.76 1 26.46 ? C3 5N6 1705 A 1 HETATM 13 C C2 5N6 . . . F 5 -2.19 -36.216 20.259 1 25.22 ? C2 5N6 1705 A 1 HETATM 14 C C1 5N6 . . . F 5 -1.157 -37.255 19.771 1 28.91 ? C1 5N6 1705 A 1 HETATM 15 O OBJ 5N6 . . . F 5 -9.251 -37.797 17.459 1 32.39 ? OBJ 5N6 1705 A 1 HETATM 16 O O9 5N6 . . . F 5 -7.709 -36.247 17.685 1 30.7 ? O9 5N6 1705 A 1 HETATM 17 O O10 5N6 . . . F 5 -6.787 -32.053 21.409 1 29.86 ? O10 5N6 1705 A 1 HETATM 18 O O7 5N6 . . . F 5 -5.702 -36.471 20.52 1 27.8 ? O7 5N6 1705 A 1 HETATM 19 O O8 5N6 . . . F 5 -5.045 -35.95 17.001 1 22.77 ? O8 5N6 1705 A 1 HETATM 20 O O4 5N6 . . . F 5 -2.292 -32.779 21.641 1 20.76 ? O4 5N6 1705 A 1 HETATM 21 O O6 5N6 . . . F 5 -3.131 -36.025 19.134 1 27.12 ? O6 5N6 1705 A 1 HETATM 22 O O1B 5N6 . . . F 5 0.064 -37.015 19.981 1 38.83 ? O1B 5N6 1705 A 1 HETATM 23 O O1A 5N6 . . . F 5 -1.526 -38.342 19.161 1 34.71 -1 O1A 5N6 1705 A 1 HETATM 24 O O2 5N6 . . . F 5 -2.914 -36.821 21.295 1 39.38 ? O2 5N6 1705 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 35 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 536 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 24 #