data_3D4P # _model_server_result.job_id lGhnWbnXpZt7JVVbYnNv-g _model_server_result.datetime_utc '2025-02-27 12:19:22' _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 3d4p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":319}' # _entry.id 3D4P # _exptl.entry_id 3D4P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 88.062 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PYRUVIC ACID' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 128.9 _cell.angle_gamma 90 _cell.entry_id 3D4P _cell.length_a 130.868 _cell.length_b 74.916 _cell.length_c 95.874 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D4P _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1,2 A,C,D,G 2 1,2 B,E,F,H 3 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 70.66267 0 74.613284 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N # _chem_comp.formula 'C3 H4 O3' _chem_comp.formula_weight 88.062 _chem_comp.id PYR _chem_comp.mon_nstd_flag . _chem_comp.name 'PYRUVIC ACID' _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 C O PYR doub 352 n n C OXT PYR sing 353 n n C CA PYR sing 354 n n OXT HXT PYR sing 355 n n CA O3 PYR doub 356 n n CA CB PYR sing 357 n n CB HB1 PYR sing 358 n n CB HB2 PYR sing 359 n n CB HB3 PYR sing 360 n n # _atom_sites.entry_id 3D4P _atom_sites.fract_transf_matrix[1][1] 0.007641 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006166 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013348 _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] 0.013402 _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 2 NAD A 1 318 1 NAD NAD . D 3 PYR A 1 319 2 PYR PYR . E 2 NAD B 1 318 1 NAD NAD . F 3 PYR B 1 319 2 PYR PYR . G 4 HOH A 1 320 13 HOH HOH . G 4 HOH A 2 321 14 HOH HOH . G 4 HOH A 3 322 15 HOH HOH . G 4 HOH A 4 323 16 HOH HOH . G 4 HOH A 5 324 17 HOH HOH . G 4 HOH A 6 325 18 HOH HOH . G 4 HOH A 7 326 19 HOH HOH . G 4 HOH A 8 327 20 HOH HOH . G 4 HOH A 9 328 22 HOH HOH . G 4 HOH A 10 329 25 HOH HOH . G 4 HOH A 11 330 26 HOH HOH . G 4 HOH A 12 331 27 HOH HOH . G 4 HOH A 13 332 28 HOH HOH . G 4 HOH A 14 333 29 HOH HOH . G 4 HOH A 15 334 30 HOH HOH . G 4 HOH A 16 335 44 HOH HOH . G 4 HOH A 17 336 45 HOH HOH . G 4 HOH A 18 337 46 HOH HOH . G 4 HOH A 19 338 47 HOH HOH . G 4 HOH A 20 339 49 HOH HOH . G 4 HOH A 21 340 50 HOH HOH . G 4 HOH A 22 341 51 HOH HOH . G 4 HOH A 23 342 56 HOH HOH . G 4 HOH A 24 343 58 HOH HOH . G 4 HOH A 25 344 63 HOH HOH . G 4 HOH A 26 345 64 HOH HOH . G 4 HOH A 27 346 66 HOH HOH . G 4 HOH A 28 347 67 HOH HOH . G 4 HOH A 29 348 69 HOH HOH . G 4 HOH A 30 349 73 HOH HOH . G 4 HOH A 31 350 75 HOH HOH . G 4 HOH A 32 351 76 HOH HOH . G 4 HOH A 33 352 78 HOH HOH . G 4 HOH A 34 353 79 HOH HOH . G 4 HOH A 35 354 81 HOH HOH . G 4 HOH A 36 355 82 HOH HOH . G 4 HOH A 37 356 84 HOH HOH . G 4 HOH A 38 357 86 HOH HOH . G 4 HOH A 39 358 88 HOH HOH . G 4 HOH A 40 359 93 HOH HOH . G 4 HOH A 41 360 95 HOH HOH . G 4 HOH A 42 361 97 HOH HOH . G 4 HOH A 43 362 98 HOH HOH . G 4 HOH A 44 363 99 HOH HOH . G 4 HOH A 45 364 100 HOH HOH . G 4 HOH A 46 365 101 HOH HOH . G 4 HOH A 47 366 102 HOH HOH . G 4 HOH A 48 367 103 HOH HOH . G 4 HOH A 49 368 105 HOH HOH . G 4 HOH A 50 369 106 HOH HOH . G 4 HOH A 51 370 107 HOH HOH . G 4 HOH A 52 371 108 HOH HOH . G 4 HOH A 53 372 112 HOH HOH . G 4 HOH A 54 373 113 HOH HOH . G 4 HOH A 55 374 118 HOH HOH . G 4 HOH A 56 375 119 HOH HOH . G 4 HOH A 57 376 122 HOH HOH . G 4 HOH A 58 377 124 HOH HOH . G 4 HOH A 59 378 127 HOH HOH . G 4 HOH A 60 379 129 HOH HOH . G 4 HOH A 61 380 130 HOH HOH . G 4 HOH A 62 381 131 HOH HOH . G 4 HOH A 63 382 132 HOH HOH . G 4 HOH A 64 383 138 HOH HOH . G 4 HOH A 65 384 139 HOH HOH . G 4 HOH A 66 385 140 HOH HOH . G 4 HOH A 67 386 141 HOH HOH . G 4 HOH A 68 387 145 HOH HOH . G 4 HOH A 69 388 148 HOH HOH . G 4 HOH A 70 389 149 HOH HOH . G 4 HOH A 71 390 150 HOH HOH . G 4 HOH A 72 391 151 HOH HOH . G 4 HOH A 73 392 152 HOH HOH . G 4 HOH A 74 393 154 HOH HOH . G 4 HOH A 75 394 156 HOH HOH . G 4 HOH A 76 395 158 HOH HOH . G 4 HOH A 77 396 162 HOH HOH . G 4 HOH A 78 397 168 HOH HOH . G 4 HOH A 79 398 169 HOH HOH . G 4 HOH A 80 399 170 HOH HOH . G 4 HOH A 81 400 172 HOH HOH . G 4 HOH A 82 401 176 HOH HOH . G 4 HOH A 83 402 178 HOH HOH . G 4 HOH A 84 403 181 HOH HOH . G 4 HOH A 85 404 182 HOH HOH . G 4 HOH A 86 405 183 HOH HOH . G 4 HOH A 87 406 184 HOH HOH . G 4 HOH A 88 407 186 HOH HOH . G 4 HOH A 89 408 188 HOH HOH . G 4 HOH A 90 409 189 HOH HOH . G 4 HOH A 91 410 190 HOH HOH . G 4 HOH A 92 411 192 HOH HOH . G 4 HOH A 93 412 194 HOH HOH . G 4 HOH A 94 413 195 HOH HOH . G 4 HOH A 95 414 197 HOH HOH . G 4 HOH A 96 415 199 HOH HOH . G 4 HOH A 97 416 203 HOH HOH . G 4 HOH A 98 417 206 HOH HOH . G 4 HOH A 99 418 211 HOH HOH . G 4 HOH A 100 419 212 HOH HOH . G 4 HOH A 101 420 214 HOH HOH . G 4 HOH A 102 421 216 HOH HOH . G 4 HOH A 103 422 220 HOH HOH . G 4 HOH A 104 423 221 HOH HOH . G 4 HOH A 105 424 222 HOH HOH . G 4 HOH A 106 425 225 HOH HOH . G 4 HOH A 107 426 227 HOH HOH . G 4 HOH A 108 427 228 HOH HOH . G 4 HOH A 109 428 230 HOH HOH . G 4 HOH A 110 429 235 HOH HOH . G 4 HOH A 111 430 236 HOH HOH . G 4 HOH A 112 431 237 HOH HOH . G 4 HOH A 113 432 238 HOH HOH . G 4 HOH A 114 433 242 HOH HOH . G 4 HOH A 115 434 243 HOH HOH . G 4 HOH A 116 435 245 HOH HOH . G 4 HOH A 117 436 246 HOH HOH . G 4 HOH A 118 437 248 HOH HOH . G 4 HOH A 119 438 250 HOH HOH . G 4 HOH A 120 439 254 HOH HOH . G 4 HOH A 121 440 257 HOH HOH . G 4 HOH A 122 441 258 HOH HOH . G 4 HOH A 123 442 261 HOH HOH . G 4 HOH A 124 443 262 HOH HOH . G 4 HOH A 125 444 263 HOH HOH . G 4 HOH A 126 445 265 HOH HOH . G 4 HOH A 127 446 267 HOH HOH . G 4 HOH A 128 447 268 HOH HOH . G 4 HOH A 129 448 269 HOH HOH . G 4 HOH A 130 449 273 HOH HOH . G 4 HOH A 131 450 274 HOH HOH . G 4 HOH A 132 451 276 HOH HOH . G 4 HOH A 133 452 282 HOH HOH . G 4 HOH A 134 453 283 HOH HOH . G 4 HOH A 135 454 284 HOH HOH . G 4 HOH A 136 455 285 HOH HOH . G 4 HOH A 137 456 286 HOH HOH . G 4 HOH A 138 457 287 HOH HOH . G 4 HOH A 139 458 289 HOH HOH . G 4 HOH A 140 459 293 HOH HOH . G 4 HOH A 141 460 294 HOH HOH . G 4 HOH A 142 461 295 HOH HOH . G 4 HOH A 143 462 296 HOH HOH . G 4 HOH A 144 463 297 HOH HOH . G 4 HOH A 145 464 298 HOH HOH . G 4 HOH A 146 465 299 HOH HOH . G 4 HOH A 147 466 300 HOH HOH . G 4 HOH A 148 467 301 HOH HOH . G 4 HOH A 149 468 303 HOH HOH . G 4 HOH A 150 469 304 HOH HOH . G 4 HOH A 151 470 305 HOH HOH . G 4 HOH A 152 471 306 HOH HOH . G 4 HOH A 153 472 307 HOH HOH . G 4 HOH A 154 473 318 HOH HOH . G 4 HOH A 155 474 319 HOH HOH . H 4 HOH B 1 320 1 HOH HOH . H 4 HOH B 2 321 2 HOH HOH . H 4 HOH B 3 322 3 HOH HOH . H 4 HOH B 4 323 4 HOH HOH . H 4 HOH B 5 324 5 HOH HOH . H 4 HOH B 6 325 6 HOH HOH . H 4 HOH B 7 326 7 HOH HOH . H 4 HOH B 8 327 8 HOH HOH . H 4 HOH B 9 328 9 HOH HOH . H 4 HOH B 10 329 10 HOH HOH . H 4 HOH B 11 330 11 HOH HOH . H 4 HOH B 12 331 12 HOH HOH . H 4 HOH B 13 332 23 HOH HOH . H 4 HOH B 14 333 24 HOH HOH . H 4 HOH B 15 334 31 HOH HOH . H 4 HOH B 16 335 32 HOH HOH . H 4 HOH B 17 336 34 HOH HOH . H 4 HOH B 18 337 35 HOH HOH . H 4 HOH B 19 338 36 HOH HOH . H 4 HOH B 20 339 37 HOH HOH . H 4 HOH B 21 340 38 HOH HOH . H 4 HOH B 22 341 40 HOH HOH . H 4 HOH B 23 342 41 HOH HOH . H 4 HOH B 24 343 42 HOH HOH . H 4 HOH B 25 344 43 HOH HOH . H 4 HOH B 26 345 48 HOH HOH . H 4 HOH B 27 346 52 HOH HOH . H 4 HOH B 28 347 53 HOH HOH . H 4 HOH B 29 348 54 HOH HOH . H 4 HOH B 30 349 55 HOH HOH . H 4 HOH B 31 350 57 HOH HOH . H 4 HOH B 32 351 59 HOH HOH . H 4 HOH B 33 352 60 HOH HOH . H 4 HOH B 34 353 62 HOH HOH . H 4 HOH B 35 354 65 HOH HOH . H 4 HOH B 36 355 68 HOH HOH . H 4 HOH B 37 356 70 HOH HOH . H 4 HOH B 38 357 71 HOH HOH . H 4 HOH B 39 358 72 HOH HOH . H 4 HOH B 40 359 74 HOH HOH . H 4 HOH B 41 360 77 HOH HOH . H 4 HOH B 42 361 80 HOH HOH . H 4 HOH B 43 362 83 HOH HOH . H 4 HOH B 44 363 85 HOH HOH . H 4 HOH B 45 364 87 HOH HOH . H 4 HOH B 46 365 89 HOH HOH . H 4 HOH B 47 366 90 HOH HOH . H 4 HOH B 48 367 92 HOH HOH . H 4 HOH B 49 368 94 HOH HOH . H 4 HOH B 50 369 96 HOH HOH . H 4 HOH B 51 370 104 HOH HOH . H 4 HOH B 52 371 109 HOH HOH . H 4 HOH B 53 372 110 HOH HOH . H 4 HOH B 54 373 111 HOH HOH . H 4 HOH B 55 374 114 HOH HOH . H 4 HOH B 56 375 115 HOH HOH . H 4 HOH B 57 376 116 HOH HOH . H 4 HOH B 58 377 117 HOH HOH . H 4 HOH B 59 378 120 HOH HOH . H 4 HOH B 60 379 121 HOH HOH . H 4 HOH B 61 380 123 HOH HOH . H 4 HOH B 62 381 125 HOH HOH . H 4 HOH B 63 382 126 HOH HOH . H 4 HOH B 64 383 128 HOH HOH . H 4 HOH B 65 384 133 HOH HOH . H 4 HOH B 66 385 134 HOH HOH . H 4 HOH B 67 386 135 HOH HOH . H 4 HOH B 68 387 136 HOH HOH . H 4 HOH B 69 388 137 HOH HOH . H 4 HOH B 70 389 142 HOH HOH . H 4 HOH B 71 390 143 HOH HOH . H 4 HOH B 72 391 144 HOH HOH . H 4 HOH B 73 392 146 HOH HOH . H 4 HOH B 74 393 147 HOH HOH . H 4 HOH B 75 394 153 HOH HOH . H 4 HOH B 76 395 155 HOH HOH . H 4 HOH B 77 396 159 HOH HOH . H 4 HOH B 78 397 160 HOH HOH . H 4 HOH B 79 398 161 HOH HOH . H 4 HOH B 80 399 163 HOH HOH . H 4 HOH B 81 400 164 HOH HOH . H 4 HOH B 82 401 165 HOH HOH . H 4 HOH B 83 402 166 HOH HOH . H 4 HOH B 84 403 167 HOH HOH . H 4 HOH B 85 404 171 HOH HOH . H 4 HOH B 86 405 173 HOH HOH . H 4 HOH B 87 406 174 HOH HOH . H 4 HOH B 88 407 175 HOH HOH . H 4 HOH B 89 408 177 HOH HOH . H 4 HOH B 90 409 179 HOH HOH . H 4 HOH B 91 410 180 HOH HOH . H 4 HOH B 92 411 187 HOH HOH . H 4 HOH B 93 412 191 HOH HOH . H 4 HOH B 94 413 196 HOH HOH . H 4 HOH B 95 414 198 HOH HOH . H 4 HOH B 96 415 200 HOH HOH . H 4 HOH B 97 416 201 HOH HOH . H 4 HOH B 98 417 202 HOH HOH . H 4 HOH B 99 418 204 HOH HOH . H 4 HOH B 100 419 205 HOH HOH . H 4 HOH B 101 420 208 HOH HOH . H 4 HOH B 102 421 209 HOH HOH . H 4 HOH B 103 422 210 HOH HOH . H 4 HOH B 104 423 213 HOH HOH . H 4 HOH B 105 424 215 HOH HOH . H 4 HOH B 106 425 217 HOH HOH . H 4 HOH B 107 426 218 HOH HOH . H 4 HOH B 108 427 223 HOH HOH . H 4 HOH B 109 428 224 HOH HOH . H 4 HOH B 110 429 226 HOH HOH . H 4 HOH B 111 430 229 HOH HOH . H 4 HOH B 112 431 231 HOH HOH . H 4 HOH B 113 432 232 HOH HOH . H 4 HOH B 114 433 233 HOH HOH . H 4 HOH B 115 434 239 HOH HOH . H 4 HOH B 116 435 240 HOH HOH . H 4 HOH B 117 436 241 HOH HOH . H 4 HOH B 118 437 244 HOH HOH . H 4 HOH B 119 438 247 HOH HOH . H 4 HOH B 120 439 249 HOH HOH . H 4 HOH B 121 440 251 HOH HOH . H 4 HOH B 122 441 252 HOH HOH . H 4 HOH B 123 442 253 HOH HOH . H 4 HOH B 124 443 255 HOH HOH . H 4 HOH B 125 444 256 HOH HOH . H 4 HOH B 126 445 259 HOH HOH . H 4 HOH B 127 446 264 HOH HOH . H 4 HOH B 128 447 266 HOH HOH . H 4 HOH B 129 448 270 HOH HOH . H 4 HOH B 130 449 271 HOH HOH . H 4 HOH B 131 450 272 HOH HOH . H 4 HOH B 132 451 275 HOH HOH . H 4 HOH B 133 452 277 HOH HOH . H 4 HOH B 134 453 278 HOH HOH . H 4 HOH B 135 454 280 HOH HOH . H 4 HOH B 136 455 281 HOH HOH . H 4 HOH B 137 456 288 HOH HOH . H 4 HOH B 138 457 290 HOH HOH . H 4 HOH B 139 458 291 HOH HOH . H 4 HOH B 140 459 302 HOH HOH . H 4 HOH B 141 460 308 HOH HOH . H 4 HOH B 142 461 309 HOH HOH . H 4 HOH B 143 462 310 HOH HOH . H 4 HOH B 144 463 311 HOH HOH . H 4 HOH B 145 464 312 HOH HOH . H 4 HOH B 146 465 313 HOH HOH . H 4 HOH B 147 466 314 HOH HOH . H 4 HOH B 148 467 315 HOH HOH . H 4 HOH B 149 468 316 HOH HOH . H 4 HOH B 150 469 317 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 C PYR . . . D 3 38.248 82.233 22.379 1 17.52 ? C PYR 319 A 1 HETATM 2 O O PYR . . . D 3 37.283 82.128 23.251 1 14.99 ? O PYR 319 A 1 HETATM 3 O OXT PYR . . . D 3 38.224 81.51 21.311 1 15.25 ? OXT PYR 319 A 1 HETATM 4 C CA PYR . . . D 3 39.274 83.17 22.504 1 19.97 ? CA PYR 319 A 1 HETATM 5 O O3 PYR . . . D 3 40.467 82.882 21.988 1 18.47 ? O3 PYR 319 A 1 HETATM 6 C CB PYR . . . D 3 38.984 84.498 23.158 1 21.3 ? CB PYR 319 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 62 _model_server_stats.create_model_time_ms 59 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 37 _model_server_stats.element_count 6 #