data_1ZVY
#
_model_server_result.job_id            UD5f-QUpxYV8eMAuMAY2MQ 
_model_server_result.datetime_utc      '2024-11-05 13:54:05' 
_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          1zvy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1758}' 
#
_entry.id    1ZVY 
#
_exptl.entry_id    1ZVY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_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          92.08 
_cell.angle_gamma         90 
_cell.entry_id            1ZVY 
_cell.length_a            43.913 
_cell.length_b            49.879 
_cell.length_c            56.995 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1ZVY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_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                      4 
_struct_asym.id                             D 
_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 22 A CYS 22 1_555 A SG CYS 96 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf2 B SG CYS 6 B CYS 6 1_555 B SG CYS 127 B CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf3 B SG CYS 30 B CYS 30 1_555 B SG CYS 115 B CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf4 B SG CYS 64 B CYS 64 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf5 B SG CYS 76 B CYS 76 1_555 B SG CYS 94 B CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
#
_chem_comp.formula           'C3 H8 O3' 
_chem_comp.formula_weight    92.094 
_chem_comp.id                GOL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              GLYCEROL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     GLYCERIN;PROPANE-1,2,3-TRIOL 
#
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 GOL sing 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     1ZVY 
_atom_sites.fract_transf_matrix[1][1]    0.02277 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00083 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.02005 
_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]    0.01756 
_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
C 3 PO4 B 1 1106 1106 PO4 PO4 . 
D 4 GOL B 1 1758 1758 GOL GOL . 
E 5 HOH A 1 137 3 HOH TIP . 
E 5 HOH A 2 138 5 HOH TIP . 
E 5 HOH A 3 139 6 HOH TIP . 
E 5 HOH A 4 140 7 HOH TIP . 
E 5 HOH A 5 141 10 HOH TIP . 
E 5 HOH A 6 142 11 HOH TIP . 
E 5 HOH A 7 143 14 HOH TIP . 
E 5 HOH A 8 144 15 HOH TIP . 
E 5 HOH A 9 145 17 HOH TIP . 
E 5 HOH A 10 146 18 HOH TIP . 
E 5 HOH A 11 147 22 HOH TIP . 
E 5 HOH A 12 148 25 HOH TIP . 
E 5 HOH A 13 149 29 HOH TIP . 
E 5 HOH A 14 150 31 HOH TIP . 
E 5 HOH A 15 151 32 HOH TIP . 
E 5 HOH A 16 152 35 HOH TIP . 
E 5 HOH A 17 153 36 HOH TIP . 
E 5 HOH A 18 154 39 HOH TIP . 
E 5 HOH A 19 155 42 HOH TIP . 
E 5 HOH A 20 156 43 HOH TIP . 
E 5 HOH A 21 157 49 HOH TIP . 
E 5 HOH A 22 158 52 HOH TIP . 
E 5 HOH A 23 159 53 HOH TIP . 
E 5 HOH A 24 160 54 HOH TIP . 
E 5 HOH A 25 161 55 HOH TIP . 
E 5 HOH A 26 162 58 HOH TIP . 
E 5 HOH A 27 163 59 HOH TIP . 
E 5 HOH A 28 164 63 HOH TIP . 
E 5 HOH A 29 165 65 HOH TIP . 
E 5 HOH A 30 166 66 HOH TIP . 
E 5 HOH A 31 167 69 HOH TIP . 
E 5 HOH A 32 168 70 HOH TIP . 
E 5 HOH A 33 169 72 HOH TIP . 
E 5 HOH A 34 170 75 HOH TIP . 
E 5 HOH A 35 171 77 HOH TIP . 
E 5 HOH A 36 172 79 HOH TIP . 
E 5 HOH A 37 173 81 HOH TIP . 
E 5 HOH A 38 174 84 HOH TIP . 
E 5 HOH A 39 175 90 HOH TIP . 
E 5 HOH A 40 176 91 HOH TIP . 
E 5 HOH A 41 177 93 HOH TIP . 
E 5 HOH A 42 178 97 HOH TIP . 
E 5 HOH A 43 179 100 HOH TIP . 
E 5 HOH A 44 180 101 HOH TIP . 
E 5 HOH A 45 181 102 HOH TIP . 
E 5 HOH A 46 182 103 HOH TIP . 
E 5 HOH A 47 183 106 HOH TIP . 
E 5 HOH A 48 184 107 HOH TIP . 
E 5 HOH A 49 185 110 HOH TIP . 
E 5 HOH A 50 186 111 HOH TIP . 
E 5 HOH A 51 187 113 HOH TIP . 
E 5 HOH A 52 188 117 HOH TIP . 
E 5 HOH A 53 189 118 HOH TIP . 
E 5 HOH A 54 190 122 HOH TIP . 
E 5 HOH A 55 191 125 HOH TIP . 
E 5 HOH A 56 192 126 HOH TIP . 
E 5 HOH A 57 193 130 HOH TIP . 
E 5 HOH A 58 194 131 HOH TIP . 
E 5 HOH A 59 195 133 HOH TIP . 
E 5 HOH A 60 196 137 HOH TIP . 
E 5 HOH A 61 197 138 HOH TIP . 
E 5 HOH A 62 198 140 HOH TIP . 
E 5 HOH A 63 199 142 HOH TIP . 
E 5 HOH A 64 200 144 HOH TIP . 
E 5 HOH A 65 201 149 HOH TIP . 
E 5 HOH A 66 202 150 HOH TIP . 
E 5 HOH A 67 203 153 HOH TIP . 
E 5 HOH A 68 204 154 HOH TIP . 
E 5 HOH A 69 205 158 HOH TIP . 
E 5 HOH A 70 206 159 HOH TIP . 
E 5 HOH A 71 207 160 HOH TIP . 
E 5 HOH A 72 208 161 HOH TIP . 
E 5 HOH A 73 209 164 HOH TIP . 
E 5 HOH A 74 210 167 HOH TIP . 
E 5 HOH A 75 211 168 HOH TIP . 
E 5 HOH A 76 212 170 HOH TIP . 
E 5 HOH A 77 213 173 HOH TIP . 
E 5 HOH A 78 214 174 HOH TIP . 
E 5 HOH A 79 215 175 HOH TIP . 
E 5 HOH A 80 216 176 HOH TIP . 
E 5 HOH A 81 217 178 HOH TIP . 
E 5 HOH A 82 218 179 HOH TIP . 
E 5 HOH A 83 219 185 HOH TIP . 
E 5 HOH A 84 220 186 HOH TIP . 
E 5 HOH A 85 221 190 HOH TIP . 
E 5 HOH A 86 222 191 HOH TIP . 
E 5 HOH A 87 223 195 HOH TIP . 
E 5 HOH A 88 224 196 HOH TIP . 
E 5 HOH A 89 225 203 HOH TIP . 
E 5 HOH A 90 226 207 HOH TIP . 
E 5 HOH A 91 227 208 HOH TIP . 
E 5 HOH A 92 228 210 HOH TIP . 
E 5 HOH A 93 229 212 HOH TIP . 
E 5 HOH A 94 230 216 HOH TIP . 
E 5 HOH A 95 231 218 HOH TIP . 
E 5 HOH A 96 232 222 HOH TIP . 
F 5 HOH B 1 1759 1 HOH TIP . 
F 5 HOH B 2 1760 2 HOH TIP . 
F 5 HOH B 3 1761 4 HOH TIP . 
F 5 HOH B 4 1762 8 HOH TIP . 
F 5 HOH B 5 1763 9 HOH TIP . 
F 5 HOH B 6 1764 12 HOH TIP . 
F 5 HOH B 7 1765 13 HOH TIP . 
F 5 HOH B 8 1766 16 HOH TIP . 
F 5 HOH B 9 1767 19 HOH TIP . 
F 5 HOH B 10 1768 20 HOH TIP . 
F 5 HOH B 11 1769 21 HOH TIP . 
F 5 HOH B 12 1770 23 HOH TIP . 
F 5 HOH B 13 1771 24 HOH TIP . 
F 5 HOH B 14 1772 26 HOH TIP . 
F 5 HOH B 15 1773 27 HOH TIP . 
F 5 HOH B 16 1774 28 HOH TIP . 
F 5 HOH B 17 1775 30 HOH TIP . 
F 5 HOH B 18 1776 33 HOH TIP . 
F 5 HOH B 19 1777 34 HOH TIP . 
F 5 HOH B 20 1778 37 HOH TIP . 
F 5 HOH B 21 1779 38 HOH TIP . 
F 5 HOH B 22 1780 40 HOH TIP . 
F 5 HOH B 23 1781 41 HOH TIP . 
F 5 HOH B 24 1782 44 HOH TIP . 
F 5 HOH B 25 1783 45 HOH TIP . 
F 5 HOH B 26 1784 46 HOH TIP . 
F 5 HOH B 27 1785 47 HOH TIP . 
F 5 HOH B 28 1786 48 HOH TIP . 
F 5 HOH B 29 1787 50 HOH TIP . 
F 5 HOH B 30 1788 51 HOH TIP . 
F 5 HOH B 31 1789 56 HOH TIP . 
F 5 HOH B 32 1790 57 HOH TIP . 
F 5 HOH B 33 1791 60 HOH TIP . 
F 5 HOH B 34 1792 61 HOH TIP . 
F 5 HOH B 35 1793 62 HOH TIP . 
F 5 HOH B 36 1794 64 HOH TIP . 
F 5 HOH B 37 1795 67 HOH TIP . 
F 5 HOH B 38 1796 68 HOH TIP . 
F 5 HOH B 39 1797 71 HOH TIP . 
F 5 HOH B 40 1798 73 HOH TIP . 
F 5 HOH B 41 1799 74 HOH TIP . 
F 5 HOH B 42 1800 76 HOH TIP . 
F 5 HOH B 43 1801 78 HOH TIP . 
F 5 HOH B 44 1802 80 HOH TIP . 
F 5 HOH B 45 1803 82 HOH TIP . 
F 5 HOH B 46 1804 83 HOH TIP . 
F 5 HOH B 47 1805 85 HOH TIP . 
F 5 HOH B 48 1806 86 HOH TIP . 
F 5 HOH B 49 1807 87 HOH TIP . 
F 5 HOH B 50 1808 88 HOH TIP . 
F 5 HOH B 51 1809 89 HOH TIP . 
F 5 HOH B 52 1810 92 HOH TIP . 
F 5 HOH B 53 1811 94 HOH TIP . 
F 5 HOH B 54 1812 95 HOH TIP . 
F 5 HOH B 55 1813 96 HOH TIP . 
F 5 HOH B 56 1814 98 HOH TIP . 
F 5 HOH B 57 1815 99 HOH TIP . 
F 5 HOH B 58 1816 104 HOH TIP . 
F 5 HOH B 59 1817 105 HOH TIP . 
F 5 HOH B 60 1818 108 HOH TIP . 
F 5 HOH B 61 1819 109 HOH TIP . 
F 5 HOH B 62 1820 112 HOH TIP . 
F 5 HOH B 63 1821 114 HOH TIP . 
F 5 HOH B 64 1822 115 HOH TIP . 
F 5 HOH B 65 1823 116 HOH TIP . 
F 5 HOH B 66 1824 119 HOH TIP . 
F 5 HOH B 67 1825 120 HOH TIP . 
F 5 HOH B 68 1826 121 HOH TIP . 
F 5 HOH B 69 1827 123 HOH TIP . 
F 5 HOH B 70 1828 124 HOH TIP . 
F 5 HOH B 71 1829 132 HOH TIP . 
F 5 HOH B 72 1830 134 HOH TIP . 
F 5 HOH B 73 1831 135 HOH TIP . 
F 5 HOH B 74 1832 136 HOH TIP . 
F 5 HOH B 75 1833 139 HOH TIP . 
F 5 HOH B 76 1834 141 HOH TIP . 
F 5 HOH B 77 1835 143 HOH TIP . 
F 5 HOH B 78 1836 145 HOH TIP . 
F 5 HOH B 79 1837 146 HOH TIP . 
F 5 HOH B 80 1838 147 HOH TIP . 
F 5 HOH B 81 1839 148 HOH TIP . 
F 5 HOH B 82 1840 151 HOH TIP . 
F 5 HOH B 83 1841 152 HOH TIP . 
F 5 HOH B 84 1842 155 HOH TIP . 
F 5 HOH B 85 1843 156 HOH TIP . 
F 5 HOH B 86 1844 157 HOH TIP . 
F 5 HOH B 87 1845 162 HOH TIP . 
F 5 HOH B 88 1846 163 HOH TIP . 
F 5 HOH B 89 1847 165 HOH TIP . 
F 5 HOH B 90 1848 166 HOH TIP . 
F 5 HOH B 91 1849 169 HOH TIP . 
F 5 HOH B 92 1850 171 HOH TIP . 
F 5 HOH B 93 1851 172 HOH TIP . 
F 5 HOH B 94 1852 177 HOH TIP . 
F 5 HOH B 95 1853 180 HOH TIP . 
F 5 HOH B 96 1854 181 HOH TIP . 
F 5 HOH B 97 1855 182 HOH TIP . 
F 5 HOH B 98 1856 183 HOH TIP . 
F 5 HOH B 99 1857 184 HOH TIP . 
F 5 HOH B 100 1858 187 HOH TIP . 
F 5 HOH B 101 1859 188 HOH TIP . 
F 5 HOH B 102 1860 189 HOH TIP . 
F 5 HOH B 103 1861 192 HOH TIP . 
F 5 HOH B 104 1862 193 HOH TIP . 
F 5 HOH B 105 1863 194 HOH TIP . 
F 5 HOH B 106 1864 198 HOH TIP . 
F 5 HOH B 107 1865 199 HOH TIP . 
F 5 HOH B 108 1866 200 HOH TIP . 
F 5 HOH B 109 1867 202 HOH TIP . 
F 5 HOH B 110 1868 204 HOH TIP . 
F 5 HOH B 111 1869 205 HOH TIP . 
F 5 HOH B 112 1870 206 HOH TIP . 
F 5 HOH B 113 1871 209 HOH TIP . 
F 5 HOH B 114 1872 211 HOH TIP . 
F 5 HOH B 115 1873 213 HOH TIP . 
F 5 HOH B 116 1874 214 HOH TIP . 
F 5 HOH B 117 1875 217 HOH TIP . 
F 5 HOH B 118 1876 220 HOH TIP . 
F 5 HOH B 119 1877 221 HOH TIP . 
F 5 HOH B 120 1878 223 HOH TIP . 
F 5 HOH B 121 1879 224 HOH TIP . 
F 5 HOH B 122 1880 225 HOH TIP . 
#
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 GOL . . . D 4 49.11 74.859 41.746 1 34.34 ? C1 GOL 1758 B 1 
HETATM 2 O O1 GOL . . . D 4 47.793 75.346 41.983 1 25.95 ? O1 GOL 1758 B 1 
HETATM 3 C C2 GOL . . . D 4 49.259 74.769 40.354 1 35.46 ? C2 GOL 1758 B 1 
HETATM 4 O O2 GOL . . . D 4 50.036 75.807 39.701 1 37.49 ? O2 GOL 1758 B 1 
HETATM 5 C C3 GOL . . . D 4 48.674 73.718 39.521 1 37.36 ? C3 GOL 1758 B 1 
HETATM 6 O O3 GOL . . . D 4 47.869 72.684 40.184 1 38.62 ? O3 GOL 1758 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#