data_5E9Y # _model_server_result.job_id dmPTBJ_L5yHEnfDQiGMLVQ _model_server_result.datetime_utc '2025-06-30 16:31:16' _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 5e9y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2001}' # _entry.id 5E9Y # _exptl.entry_id 5E9Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _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 5E9Y _cell.length_a 81.317 _cell.length_b 96.19 _cell.length_c 57.749 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5E9Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 _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 # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MPD _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL _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 MPD sing 237 n n C1 H11 MPD sing 238 n n C1 H12 MPD sing 239 n n C1 H13 MPD sing 240 n n C2 O2 MPD sing 241 n n C2 CM MPD sing 242 n n C2 C3 MPD sing 243 n n O2 HO2 MPD sing 244 n n CM HM1 MPD sing 245 n n CM HM2 MPD sing 246 n n CM HM3 MPD sing 247 n n C3 C4 MPD sing 248 n n C3 H31 MPD sing 249 n n C3 H32 MPD sing 250 n n C4 O4 MPD sing 251 n n C4 C5 MPD sing 252 n n C4 H4 MPD sing 253 n n O4 HO4 MPD sing 254 n n C5 H51 MPD sing 255 n n C5 H52 MPD sing 256 n n C5 H53 MPD sing 257 n n # _atom_sites.entry_id 5E9Y _atom_sites.fract_transf_matrix[1][1] 0.012298 _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] 0.010396 _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] 0.017316 _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 MPD A 1 2001 1 MPD MPD . C 3 HOH A 1 2101 43 HOH HOH . C 3 HOH A 2 2102 122 HOH HOH . C 3 HOH A 3 2103 26 HOH HOH . C 3 HOH A 4 2104 52 HOH HOH . C 3 HOH A 5 2105 88 HOH HOH . C 3 HOH A 6 2106 107 HOH HOH . C 3 HOH A 7 2107 82 HOH HOH . C 3 HOH A 8 2108 78 HOH HOH . C 3 HOH A 9 2109 118 HOH HOH . C 3 HOH A 10 2110 59 HOH HOH . C 3 HOH A 11 2111 51 HOH HOH . C 3 HOH A 12 2112 153 HOH HOH . C 3 HOH A 13 2113 97 HOH HOH . C 3 HOH A 14 2114 7 HOH HOH . C 3 HOH A 15 2115 36 HOH HOH . C 3 HOH A 16 2116 31 HOH HOH . C 3 HOH A 17 2117 123 HOH HOH . C 3 HOH A 18 2118 39 HOH HOH . C 3 HOH A 19 2119 15 HOH HOH . C 3 HOH A 20 2120 22 HOH HOH . C 3 HOH A 21 2121 4 HOH HOH . C 3 HOH A 22 2122 23 HOH HOH . C 3 HOH A 23 2123 63 HOH HOH . C 3 HOH A 24 2124 69 HOH HOH . C 3 HOH A 25 2125 32 HOH HOH . C 3 HOH A 26 2126 47 HOH HOH . C 3 HOH A 27 2127 90 HOH HOH . C 3 HOH A 28 2128 19 HOH HOH . C 3 HOH A 29 2129 16 HOH HOH . C 3 HOH A 30 2130 3 HOH HOH . C 3 HOH A 31 2131 74 HOH HOH . C 3 HOH A 32 2132 46 HOH HOH . C 3 HOH A 33 2133 17 HOH HOH . C 3 HOH A 34 2134 85 HOH HOH . C 3 HOH A 35 2135 95 HOH HOH . C 3 HOH A 36 2136 89 HOH HOH . C 3 HOH A 37 2137 30 HOH HOH . C 3 HOH A 38 2138 87 HOH HOH . C 3 HOH A 39 2139 24 HOH HOH . C 3 HOH A 40 2140 18 HOH HOH . C 3 HOH A 41 2141 35 HOH HOH . C 3 HOH A 42 2142 48 HOH HOH . C 3 HOH A 43 2143 25 HOH HOH . C 3 HOH A 44 2144 71 HOH HOH . C 3 HOH A 45 2145 38 HOH HOH . C 3 HOH A 46 2146 8 HOH HOH . C 3 HOH A 47 2147 20 HOH HOH . C 3 HOH A 48 2148 12 HOH HOH . C 3 HOH A 49 2149 44 HOH HOH . C 3 HOH A 50 2150 41 HOH HOH . C 3 HOH A 51 2151 145 HOH HOH . C 3 HOH A 52 2152 34 HOH HOH . C 3 HOH A 53 2153 148 HOH HOH . C 3 HOH A 54 2154 37 HOH HOH . C 3 HOH A 55 2155 49 HOH HOH . C 3 HOH A 56 2156 50 HOH HOH . C 3 HOH A 57 2157 77 HOH HOH . C 3 HOH A 58 2158 54 HOH HOH . C 3 HOH A 59 2159 28 HOH HOH . C 3 HOH A 60 2160 56 HOH HOH . C 3 HOH A 61 2161 150 HOH HOH . C 3 HOH A 62 2162 10 HOH HOH . C 3 HOH A 63 2163 6 HOH HOH . C 3 HOH A 64 2164 125 HOH HOH . C 3 HOH A 65 2165 64 HOH HOH . C 3 HOH A 66 2166 5 HOH HOH . C 3 HOH A 67 2167 58 HOH HOH . C 3 HOH A 68 2168 2 HOH HOH . C 3 HOH A 69 2169 110 HOH HOH . C 3 HOH A 70 2170 101 HOH HOH . C 3 HOH A 71 2171 55 HOH HOH . C 3 HOH A 72 2172 132 HOH HOH . C 3 HOH A 73 2173 91 HOH HOH . C 3 HOH A 74 2174 33 HOH HOH . C 3 HOH A 75 2175 115 HOH HOH . C 3 HOH A 76 2176 80 HOH HOH . C 3 HOH A 77 2177 81 HOH HOH . C 3 HOH A 78 2178 62 HOH HOH . C 3 HOH A 79 2179 111 HOH HOH . C 3 HOH A 80 2180 29 HOH HOH . C 3 HOH A 81 2181 103 HOH HOH . C 3 HOH A 82 2182 1 HOH HOH . C 3 HOH A 83 2183 124 HOH HOH . C 3 HOH A 84 2184 79 HOH HOH . C 3 HOH A 85 2185 109 HOH HOH . C 3 HOH A 86 2186 13 HOH HOH . C 3 HOH A 87 2187 129 HOH HOH . C 3 HOH A 88 2188 27 HOH HOH . C 3 HOH A 89 2189 14 HOH HOH . C 3 HOH A 90 2190 53 HOH HOH . C 3 HOH A 91 2191 45 HOH HOH . C 3 HOH A 92 2192 60 HOH HOH . C 3 HOH A 93 2193 119 HOH HOH . C 3 HOH A 94 2194 130 HOH HOH . C 3 HOH A 95 2195 102 HOH HOH . C 3 HOH A 96 2196 9 HOH HOH . C 3 HOH A 97 2197 40 HOH HOH . C 3 HOH A 98 2198 99 HOH HOH . C 3 HOH A 99 2199 106 HOH HOH . C 3 HOH A 100 2200 75 HOH HOH . C 3 HOH A 101 2201 70 HOH HOH . C 3 HOH A 102 2202 96 HOH HOH . C 3 HOH A 103 2203 147 HOH HOH . C 3 HOH A 104 2204 11 HOH HOH . C 3 HOH A 105 2205 98 HOH HOH . C 3 HOH A 106 2206 76 HOH HOH . C 3 HOH A 107 2207 116 HOH HOH . C 3 HOH A 108 2208 93 HOH HOH . C 3 HOH A 109 2209 155 HOH HOH . C 3 HOH A 110 2210 149 HOH HOH . C 3 HOH A 111 2211 67 HOH HOH . C 3 HOH A 112 2212 121 HOH HOH . C 3 HOH A 113 2213 66 HOH HOH . C 3 HOH A 114 2214 144 HOH HOH . C 3 HOH A 115 2215 143 HOH HOH . C 3 HOH A 116 2216 152 HOH HOH . C 3 HOH A 117 2217 57 HOH HOH . C 3 HOH A 118 2218 68 HOH HOH . C 3 HOH A 119 2219 73 HOH HOH . C 3 HOH A 120 2220 138 HOH HOH . C 3 HOH A 121 2221 133 HOH HOH . C 3 HOH A 122 2222 146 HOH HOH . C 3 HOH A 123 2223 86 HOH HOH . C 3 HOH A 124 2224 61 HOH HOH . C 3 HOH A 125 2225 142 HOH HOH . C 3 HOH A 126 2226 42 HOH HOH . C 3 HOH A 127 2227 65 HOH HOH . C 3 HOH A 128 2228 100 HOH HOH . C 3 HOH A 129 2229 154 HOH HOH . C 3 HOH A 130 2230 83 HOH HOH . C 3 HOH A 131 2231 114 HOH HOH . C 3 HOH A 132 2232 21 HOH HOH . C 3 HOH A 133 2233 104 HOH HOH . C 3 HOH A 134 2234 117 HOH HOH . C 3 HOH A 135 2235 120 HOH HOH . C 3 HOH A 136 2236 92 HOH HOH . C 3 HOH A 137 2237 140 HOH HOH . C 3 HOH A 138 2238 108 HOH HOH . C 3 HOH A 139 2239 72 HOH HOH . C 3 HOH A 140 2240 112 HOH HOH . C 3 HOH A 141 2241 84 HOH HOH . C 3 HOH A 142 2242 156 HOH HOH . C 3 HOH A 143 2243 139 HOH HOH . C 3 HOH A 144 2244 113 HOH HOH . C 3 HOH A 145 2245 131 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 MPD . . . B 2 -26.404 -6.481 -0.25 1 57.97 ? C1 MPD 2001 A 1 HETATM 2 C C2 MPD . . . B 2 -26.961 -7.007 1.066 1 57.11 ? C2 MPD 2001 A 1 HETATM 3 O O2 MPD . . . B 2 -26.247 -6.39 2.168 1 51.38 ? O2 MPD 2001 A 1 HETATM 4 C CM MPD . . . B 2 -28.43 -6.61 1.183 1 63.46 ? CM MPD 2001 A 1 HETATM 5 C C3 MPD . . . B 2 -26.826 -8.529 1.147 1 51.01 ? C3 MPD 2001 A 1 HETATM 6 C C4 MPD . . . B 2 -25.505 -9.063 0.589 1 41.02 ? C4 MPD 2001 A 1 HETATM 7 O O4 MPD . . . B 2 -24.401 -8.499 1.261 1 33.02 ? O4 MPD 2001 A 1 HETATM 8 C C5 MPD . . . B 2 -25.431 -10.585 0.693 1 39.73 ? C5 MPD 2001 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 8 #