data_5YDB # _model_server_result.job_id X0dF9kZr93JM5aZM8Oy-Yg _model_server_result.datetime_utc '2024-12-02 04:58:19' _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 5ydb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":202}' # _entry.id 5YDB # _exptl.entry_id 5YDB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 190.151 _entity.id 3 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description '1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID' _entity.pdbx_number_of_molecules 4 _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 5YDB _cell.length_a 139.117 _cell.length_b 139.117 _cell.length_c 79.587 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YDB _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,G,H,I,J,K,L,M,N,O,P _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 H N N ? 3 J N N ? 3 L N N # _chem_comp.formula 'C7 H10 O6' _chem_comp.formula_weight 190.151 _chem_comp.id DQA _chem_comp.mon_nstd_flag . _chem_comp.name '1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '3-DEHYDROQUINIC 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 C1 C2 DQA sing 83 n n C1 C6 DQA sing 84 n n C1 C DQA sing 85 n n C1 O6 DQA sing 86 n n C2 C3 DQA sing 87 n n C2 H21 DQA sing 88 n n C2 H22 DQA sing 89 n n C3 O3 DQA sing 90 n n C3 C4 DQA sing 91 n n C3 H3 DQA sing 92 n n O3 HO3 DQA sing 93 n n C4 O4 DQA sing 94 n n C4 C5 DQA sing 95 n n C4 H4 DQA sing 96 n n O4 HO4 DQA sing 97 n n C5 C6 DQA sing 98 n n C5 O5 DQA doub 99 n n C6 H61 DQA sing 100 n n C6 H62 DQA sing 101 n n C O1 DQA doub 102 n n C O2 DQA sing 103 n n O2 HO2 DQA sing 104 n n O6 HO6 DQA sing 105 n n # _atom_sites.entry_id 5YDB _atom_sites.fract_transf_matrix[1][1] 0.007188 _atom_sites.fract_transf_matrix[1][2] 0.00415 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0083 _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] 0.012565 _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 E 2 NA A 1 201 4 NA NA . F 3 DQA A 1 202 2 DQA DQA . G 2 NA B 1 201 3 NA NA . H 3 DQA B 1 202 1 DQA DQA . I 2 NA C 1 201 2 NA NA . J 3 DQA C 1 202 3 DQA DQA . K 2 NA D 1 201 1 NA NA . L 3 DQA D 1 202 4 DQA DQA . M 4 HOH A 1 301 118 HOH HOH . M 4 HOH A 2 302 110 HOH HOH . M 4 HOH A 3 303 59 HOH HOH . M 4 HOH A 4 304 283 HOH HOH . M 4 HOH A 5 305 167 HOH HOH . M 4 HOH A 6 306 18 HOH HOH . M 4 HOH A 7 307 248 HOH HOH . M 4 HOH A 8 308 180 HOH HOH . M 4 HOH A 9 309 279 HOH HOH . M 4 HOH A 10 310 16 HOH HOH . M 4 HOH A 11 311 295 HOH HOH . M 4 HOH A 12 312 280 HOH HOH . M 4 HOH A 13 313 120 HOH HOH . M 4 HOH A 14 314 301 HOH HOH . M 4 HOH A 15 315 119 HOH HOH . M 4 HOH A 16 316 146 HOH HOH . M 4 HOH A 17 317 284 HOH HOH . M 4 HOH A 18 318 1 HOH HOH . M 4 HOH A 19 319 306 HOH HOH . M 4 HOH A 20 320 175 HOH HOH . M 4 HOH A 21 321 4 HOH HOH . M 4 HOH A 22 322 91 HOH HOH . M 4 HOH A 23 323 166 HOH HOH . M 4 HOH A 24 324 281 HOH HOH . M 4 HOH A 25 325 303 HOH HOH . M 4 HOH A 26 326 111 HOH HOH . M 4 HOH A 27 327 176 HOH HOH . M 4 HOH A 28 328 292 HOH HOH . M 4 HOH A 29 329 286 HOH HOH . M 4 HOH A 30 330 285 HOH HOH . M 4 HOH A 31 331 151 HOH HOH . M 4 HOH A 32 332 149 HOH HOH . M 4 HOH A 33 333 95 HOH HOH . M 4 HOH A 34 334 304 HOH HOH . M 4 HOH A 35 335 278 HOH HOH . M 4 HOH A 36 336 179 HOH HOH . M 4 HOH A 37 337 165 HOH HOH . M 4 HOH A 38 338 276 HOH HOH . M 4 HOH A 39 339 60 HOH HOH . M 4 HOH A 40 340 147 HOH HOH . M 4 HOH A 41 341 282 HOH HOH . M 4 HOH A 42 342 173 HOH HOH . M 4 HOH A 43 343 115 HOH HOH . M 4 HOH A 44 344 168 HOH HOH . M 4 HOH A 45 345 109 HOH HOH . M 4 HOH A 46 346 177 HOH HOH . M 4 HOH A 47 347 170 HOH HOH . M 4 HOH A 48 348 184 HOH HOH . M 4 HOH A 49 349 171 HOH HOH . M 4 HOH A 50 350 92 HOH HOH . M 4 HOH A 51 351 145 HOH HOH . M 4 HOH A 52 352 319 HOH HOH . M 4 HOH A 53 353 181 HOH HOH . M 4 HOH A 54 354 169 HOH HOH . M 4 HOH A 55 355 287 HOH HOH . M 4 HOH A 56 356 189 HOH HOH . M 4 HOH A 57 357 74 HOH HOH . M 4 HOH A 58 358 172 HOH HOH . M 4 HOH A 59 359 174 HOH HOH . N 4 HOH B 1 301 108 HOH HOH . N 4 HOH B 2 302 139 HOH HOH . N 4 HOH B 3 303 155 HOH HOH . N 4 HOH B 4 304 193 HOH HOH . N 4 HOH B 5 305 183 HOH HOH . N 4 HOH B 6 306 240 HOH HOH . N 4 HOH B 7 307 229 HOH HOH . N 4 HOH B 8 308 140 HOH HOH . N 4 HOH B 9 309 249 HOH HOH . N 4 HOH B 10 310 244 HOH HOH . N 4 HOH B 11 311 178 HOH HOH . N 4 HOH B 12 312 37 HOH HOH . N 4 HOH B 13 313 219 HOH HOH . N 4 HOH B 14 314 247 HOH HOH . N 4 HOH B 15 315 243 HOH HOH . N 4 HOH B 16 316 84 HOH HOH . N 4 HOH B 17 317 307 HOH HOH . N 4 HOH B 18 318 299 HOH HOH . N 4 HOH B 19 319 135 HOH HOH . N 4 HOH B 20 320 232 HOH HOH . N 4 HOH B 21 321 131 HOH HOH . N 4 HOH B 22 322 35 HOH HOH . N 4 HOH B 23 323 99 HOH HOH . N 4 HOH B 24 324 152 HOH HOH . N 4 HOH B 25 325 159 HOH HOH . N 4 HOH B 26 326 130 HOH HOH . N 4 HOH B 27 327 136 HOH HOH . N 4 HOH B 28 328 134 HOH HOH . N 4 HOH B 29 329 297 HOH HOH . N 4 HOH B 30 330 154 HOH HOH . N 4 HOH B 31 331 153 HOH HOH . N 4 HOH B 32 332 308 HOH HOH . N 4 HOH B 33 333 250 HOH HOH . N 4 HOH B 34 334 289 HOH HOH . N 4 HOH B 35 335 320 HOH HOH . N 4 HOH B 36 336 98 HOH HOH . N 4 HOH B 37 337 33 HOH HOH . N 4 HOH B 38 338 231 HOH HOH . N 4 HOH B 39 339 290 HOH HOH . N 4 HOH B 40 340 242 HOH HOH . N 4 HOH B 41 341 239 HOH HOH . N 4 HOH B 42 342 312 HOH HOH . N 4 HOH B 43 343 241 HOH HOH . N 4 HOH B 44 344 309 HOH HOH . N 4 HOH B 45 345 85 HOH HOH . N 4 HOH B 46 346 237 HOH HOH . N 4 HOH B 47 347 230 HOH HOH . O 4 HOH C 1 301 106 HOH HOH . O 4 HOH C 2 302 187 HOH HOH . O 4 HOH C 3 303 105 HOH HOH . O 4 HOH C 4 304 103 HOH HOH . O 4 HOH C 5 305 256 HOH HOH . O 4 HOH C 6 306 158 HOH HOH . O 4 HOH C 7 307 190 HOH HOH . O 4 HOH C 8 308 199 HOH HOH . O 4 HOH C 9 309 191 HOH HOH . O 4 HOH C 10 310 195 HOH HOH . O 4 HOH C 11 311 194 HOH HOH . O 4 HOH C 12 312 43 HOH HOH . O 4 HOH C 13 313 186 HOH HOH . O 4 HOH C 14 314 262 HOH HOH . O 4 HOH C 15 315 254 HOH HOH . O 4 HOH C 16 316 265 HOH HOH . O 4 HOH C 17 317 160 HOH HOH . O 4 HOH C 18 318 204 HOH HOH . O 4 HOH C 19 319 245 HOH HOH . O 4 HOH C 20 320 253 HOH HOH . O 4 HOH C 21 321 133 HOH HOH . O 4 HOH C 22 322 104 HOH HOH . O 4 HOH C 23 323 197 HOH HOH . O 4 HOH C 24 324 203 HOH HOH . O 4 HOH C 25 325 267 HOH HOH . O 4 HOH C 26 326 44 HOH HOH . O 4 HOH C 27 327 201 HOH HOH . O 4 HOH C 28 328 100 HOH HOH . O 4 HOH C 29 329 263 HOH HOH . O 4 HOH C 30 330 251 HOH HOH . O 4 HOH C 31 331 264 HOH HOH . O 4 HOH C 32 332 36 HOH HOH . O 4 HOH C 33 333 156 HOH HOH . O 4 HOH C 34 334 101 HOH HOH . O 4 HOH C 35 335 137 HOH HOH . O 4 HOH C 36 336 198 HOH HOH . O 4 HOH C 37 337 157 HOH HOH . O 4 HOH C 38 338 255 HOH HOH . O 4 HOH C 39 339 259 HOH HOH . O 4 HOH C 40 340 277 HOH HOH . O 4 HOH C 41 341 188 HOH HOH . O 4 HOH C 42 342 257 HOH HOH . O 4 HOH C 43 343 164 HOH HOH . O 4 HOH C 44 344 102 HOH HOH . O 4 HOH C 45 345 185 HOH HOH . O 4 HOH C 46 346 258 HOH HOH . O 4 HOH C 47 347 202 HOH HOH . O 4 HOH C 48 348 310 HOH HOH . P 4 HOH D 1 301 42 HOH HOH . P 4 HOH D 2 302 271 HOH HOH . P 4 HOH D 3 303 52 HOH HOH . P 4 HOH D 4 304 210 HOH HOH . P 4 HOH D 5 305 40 HOH HOH . P 4 HOH D 6 306 314 HOH HOH . P 4 HOH D 7 307 273 HOH HOH . P 4 HOH D 8 308 208 HOH HOH . P 4 HOH D 9 309 196 HOH HOH . P 4 HOH D 10 310 223 HOH HOH . P 4 HOH D 11 311 51 HOH HOH . P 4 HOH D 12 312 212 HOH HOH . P 4 HOH D 13 313 300 HOH HOH . P 4 HOH D 14 314 47 HOH HOH . P 4 HOH D 15 315 45 HOH HOH . P 4 HOH D 16 316 107 HOH HOH . P 4 HOH D 17 317 268 HOH HOH . P 4 HOH D 18 318 38 HOH HOH . P 4 HOH D 19 319 226 HOH HOH . P 4 HOH D 20 320 48 HOH HOH . P 4 HOH D 21 321 274 HOH HOH . P 4 HOH D 22 322 46 HOH HOH . P 4 HOH D 23 323 220 HOH HOH . P 4 HOH D 24 324 222 HOH HOH . P 4 HOH D 25 325 227 HOH HOH . P 4 HOH D 26 326 53 HOH HOH . P 4 HOH D 27 327 221 HOH HOH . P 4 HOH D 28 328 132 HOH HOH . P 4 HOH D 29 329 216 HOH HOH . P 4 HOH D 30 330 214 HOH HOH . P 4 HOH D 31 331 217 HOH HOH . P 4 HOH D 32 332 49 HOH HOH . P 4 HOH D 33 333 39 HOH HOH . P 4 HOH D 34 334 207 HOH HOH . P 4 HOH D 35 335 54 HOH HOH . P 4 HOH D 36 336 269 HOH HOH . P 4 HOH D 37 337 215 HOH HOH . P 4 HOH D 38 338 266 HOH HOH . P 4 HOH D 39 339 313 HOH HOH . P 4 HOH D 40 340 228 HOH HOH . P 4 HOH D 41 341 209 HOH HOH . P 4 HOH D 42 342 311 HOH HOH . P 4 HOH D 43 343 213 HOH HOH . P 4 HOH D 44 344 275 HOH HOH . P 4 HOH D 45 345 218 HOH HOH . P 4 HOH D 46 346 200 HOH HOH . P 4 HOH D 47 347 225 HOH HOH . P 4 HOH D 48 348 211 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 DQA . . . J 3 -23.539 9.834 -63.443 1 58.05 ? C1 DQA 202 C 1 HETATM 2 C C2 DQA . . . J 3 -22.163 9.813 -62.731 1 54.27 ? C2 DQA 202 C 1 HETATM 3 C C3 DQA . . . J 3 -21.772 8.469 -62.127 1 55.66 ? C3 DQA 202 C 1 HETATM 4 O O3 DQA . . . J 3 -20.619 8.516 -61.219 1 51.31 ? O3 DQA 202 C 1 HETATM 5 C C4 DQA . . . J 3 -22.892 7.954 -61.238 1 68.15 ? C4 DQA 202 C 1 HETATM 6 O O4 DQA . . . J 3 -22.585 6.595 -60.806 1 72.88 ? O4 DQA 202 C 1 HETATM 7 C C5 DQA . . . J 3 -24.245 8.056 -61.833 1 62.21 ? C5 DQA 202 C 1 HETATM 8 C C6 DQA . . . J 3 -24.684 9.25 -62.614 1 61.72 ? C6 DQA 202 C 1 HETATM 9 C C DQA . . . J 3 -24.083 11.213 -63.849 1 57.73 ? C DQA 202 C 1 HETATM 10 O O1 DQA . . . J 3 -24.897 11.373 -64.826 1 43.38 ? O1 DQA 202 C 1 HETATM 11 O O2 DQA . . . J 3 -23.733 12.208 -63.141 1 48.19 ? O2 DQA 202 C 1 HETATM 12 O O5 DQA . . . J 3 -25.043 7.158 -61.638 1 86.02 ? O5 DQA 202 C 1 HETATM 13 O O6 DQA . . . J 3 -23.319 9.072 -64.599 1 63.03 ? O6 DQA 202 C 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 13 #