data_3N1D # _model_server_result.job_id 5tjpcsJpXxp5GAVFsjsPoA _model_server_result.datetime_utc '2024-10-23 08:25:08' _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 3n1d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":250}' # _entry.id 3N1D # _exptl.entry_id 3N1D _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 90 _cell.angle_gamma 120 _cell.entry_id 3N1D _cell.length_a 129.968 _cell.length_b 129.968 _cell.length_c 40.244 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3N1D _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 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 _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 # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG B 1 NAG 2 n B NAG 2 B 2 NAG B 2 NAG # 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 covale ? covale1 A ND2 ASN 227 A ASN 227 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? # _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 116 n n C1 C2 GOL sing 117 n n C1 H11 GOL sing 118 n n C1 H12 GOL sing 119 n n O1 HO1 GOL sing 120 n n C2 O2 GOL sing 121 n n C2 C3 GOL sing 122 n n C2 H2 GOL sing 123 n n O2 HO2 GOL sing 124 n n C3 O3 GOL sing 125 n n C3 H31 GOL sing 126 n n C3 H32 GOL sing 127 n n O3 HO3 GOL sing 128 n n # _atom_sites.entry_id 3N1D _atom_sites.fract_transf_matrix[1][1] 0.007694 _atom_sites.fract_transf_matrix[1][2] 0.004442 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008884 _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] 0.024848 _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 RIP A 1 249 1 RIP RIP . D 4 GOL A 1 250 1 GOL GOL . E 5 PEG A 1 251 1 PEG PEG . F 6 HOH A 1 252 1 HOH HOH . F 6 HOH A 2 253 2 HOH HOH . F 6 HOH A 3 254 3 HOH HOH . F 6 HOH A 4 255 4 HOH HOH . F 6 HOH A 5 256 5 HOH HOH . F 6 HOH A 6 257 7 HOH HOH . F 6 HOH A 7 258 8 HOH HOH . F 6 HOH A 8 259 9 HOH HOH . F 6 HOH A 9 260 260 HOH HOH . F 6 HOH A 10 261 10 HOH HOH . F 6 HOH A 11 262 262 HOH HOH . F 6 HOH A 12 263 263 HOH HOH . F 6 HOH A 13 264 264 HOH HOH . F 6 HOH A 14 265 265 HOH HOH . F 6 HOH A 15 266 266 HOH HOH . F 6 HOH A 16 267 267 HOH HOH . F 6 HOH A 17 268 11 HOH HOH . F 6 HOH A 18 269 12 HOH HOH . F 6 HOH A 19 270 13 HOH HOH . F 6 HOH A 20 271 14 HOH HOH . F 6 HOH A 21 272 15 HOH HOH . F 6 HOH A 22 273 16 HOH HOH . F 6 HOH A 23 274 17 HOH HOH . F 6 HOH A 24 275 18 HOH HOH . F 6 HOH A 25 276 19 HOH HOH . F 6 HOH A 26 277 20 HOH HOH . F 6 HOH A 27 278 21 HOH HOH . F 6 HOH A 28 279 22 HOH HOH . F 6 HOH A 29 280 23 HOH HOH . F 6 HOH A 30 281 24 HOH HOH . F 6 HOH A 31 282 25 HOH HOH . F 6 HOH A 32 283 26 HOH HOH . F 6 HOH A 33 284 27 HOH HOH . F 6 HOH A 34 285 28 HOH HOH . F 6 HOH A 35 286 29 HOH HOH . F 6 HOH A 36 287 30 HOH HOH . F 6 HOH A 37 288 31 HOH HOH . F 6 HOH A 38 289 32 HOH HOH . F 6 HOH A 39 290 33 HOH HOH . F 6 HOH A 40 291 34 HOH HOH . F 6 HOH A 41 292 35 HOH HOH . F 6 HOH A 42 293 36 HOH HOH . F 6 HOH A 43 294 37 HOH HOH . F 6 HOH A 44 295 38 HOH HOH . F 6 HOH A 45 296 39 HOH HOH . F 6 HOH A 46 297 40 HOH HOH . F 6 HOH A 47 298 41 HOH HOH . F 6 HOH A 48 299 42 HOH HOH . F 6 HOH A 49 300 43 HOH HOH . F 6 HOH A 50 301 44 HOH HOH . F 6 HOH A 51 302 45 HOH HOH . F 6 HOH A 52 303 46 HOH HOH . F 6 HOH A 53 304 47 HOH HOH . F 6 HOH A 54 305 48 HOH HOH . F 6 HOH A 55 306 49 HOH HOH . F 6 HOH A 56 307 50 HOH HOH . F 6 HOH A 57 308 51 HOH HOH . F 6 HOH A 58 309 52 HOH HOH . F 6 HOH A 59 310 53 HOH HOH . F 6 HOH A 60 311 54 HOH HOH . F 6 HOH A 61 312 55 HOH HOH . F 6 HOH A 62 313 56 HOH HOH . F 6 HOH A 63 314 57 HOH HOH . F 6 HOH A 64 315 58 HOH HOH . F 6 HOH A 65 316 59 HOH HOH . F 6 HOH A 66 317 60 HOH HOH . F 6 HOH A 67 318 61 HOH HOH . F 6 HOH A 68 319 62 HOH HOH . F 6 HOH A 69 320 63 HOH HOH . F 6 HOH A 70 321 64 HOH HOH . F 6 HOH A 71 322 65 HOH HOH . F 6 HOH A 72 323 66 HOH HOH . F 6 HOH A 73 324 67 HOH HOH . F 6 HOH A 74 325 68 HOH HOH . F 6 HOH A 75 326 69 HOH HOH . F 6 HOH A 76 327 70 HOH HOH . F 6 HOH A 77 328 71 HOH HOH . F 6 HOH A 78 329 72 HOH HOH . F 6 HOH A 79 330 73 HOH HOH . F 6 HOH A 80 331 74 HOH HOH . F 6 HOH A 81 332 75 HOH HOH . F 6 HOH A 82 333 76 HOH HOH . F 6 HOH A 83 334 77 HOH HOH . F 6 HOH A 84 335 78 HOH HOH . F 6 HOH A 85 336 79 HOH HOH . F 6 HOH A 86 337 80 HOH HOH . F 6 HOH A 87 338 81 HOH HOH . F 6 HOH A 88 339 82 HOH HOH . F 6 HOH A 89 340 83 HOH HOH . F 6 HOH A 90 341 84 HOH HOH . F 6 HOH A 91 342 85 HOH HOH . F 6 HOH A 92 343 86 HOH HOH . F 6 HOH A 93 344 87 HOH HOH . F 6 HOH A 94 345 88 HOH HOH . F 6 HOH A 95 346 89 HOH HOH . F 6 HOH A 96 347 91 HOH HOH . F 6 HOH A 97 348 92 HOH HOH . F 6 HOH A 98 349 93 HOH HOH . F 6 HOH A 99 350 94 HOH HOH . F 6 HOH A 100 351 95 HOH HOH . F 6 HOH A 101 352 96 HOH HOH . F 6 HOH A 102 353 97 HOH HOH . F 6 HOH A 103 354 98 HOH HOH . F 6 HOH A 104 355 99 HOH HOH . F 6 HOH A 105 356 100 HOH HOH . F 6 HOH A 106 357 101 HOH HOH . F 6 HOH A 107 358 102 HOH HOH . F 6 HOH A 108 359 103 HOH HOH . F 6 HOH A 109 360 104 HOH HOH . F 6 HOH A 110 361 105 HOH HOH . F 6 HOH A 111 362 106 HOH HOH . F 6 HOH A 112 363 107 HOH HOH . F 6 HOH A 113 364 108 HOH HOH . F 6 HOH A 114 365 109 HOH HOH . F 6 HOH A 115 366 110 HOH HOH . F 6 HOH A 116 367 111 HOH HOH . F 6 HOH A 117 368 112 HOH HOH . F 6 HOH A 118 369 113 HOH HOH . F 6 HOH A 119 370 114 HOH HOH . F 6 HOH A 120 371 115 HOH HOH . F 6 HOH A 121 372 116 HOH HOH . F 6 HOH A 122 373 117 HOH HOH . F 6 HOH A 123 374 118 HOH HOH . F 6 HOH A 124 375 119 HOH HOH . F 6 HOH A 125 376 120 HOH HOH . F 6 HOH A 126 377 121 HOH HOH . F 6 HOH A 127 378 122 HOH HOH . F 6 HOH A 128 379 123 HOH HOH . F 6 HOH A 129 380 124 HOH HOH . F 6 HOH A 130 381 125 HOH HOH . F 6 HOH A 131 382 126 HOH HOH . F 6 HOH A 132 383 127 HOH HOH . F 6 HOH A 133 384 128 HOH HOH . F 6 HOH A 134 385 129 HOH HOH . F 6 HOH A 135 386 130 HOH HOH . F 6 HOH A 136 387 131 HOH HOH . F 6 HOH A 137 388 132 HOH HOH . F 6 HOH A 138 389 133 HOH HOH . F 6 HOH A 139 390 134 HOH HOH . F 6 HOH A 140 391 135 HOH HOH . F 6 HOH A 141 392 136 HOH HOH . F 6 HOH A 142 393 137 HOH HOH . F 6 HOH A 143 394 138 HOH HOH . F 6 HOH A 144 395 139 HOH HOH . F 6 HOH A 145 396 140 HOH HOH . F 6 HOH A 146 397 141 HOH HOH . F 6 HOH A 147 398 142 HOH HOH . F 6 HOH A 148 399 143 HOH HOH . F 6 HOH A 149 400 144 HOH HOH . F 6 HOH A 150 401 145 HOH HOH . F 6 HOH A 151 402 146 HOH HOH . F 6 HOH A 152 403 147 HOH HOH . F 6 HOH A 153 404 148 HOH HOH . F 6 HOH A 154 405 149 HOH HOH . F 6 HOH A 155 406 150 HOH HOH . F 6 HOH A 156 407 151 HOH HOH . F 6 HOH A 157 408 152 HOH HOH . F 6 HOH A 158 409 153 HOH HOH . F 6 HOH A 159 410 154 HOH HOH . F 6 HOH A 160 411 156 HOH HOH . F 6 HOH A 161 412 157 HOH HOH . F 6 HOH A 162 413 158 HOH HOH . F 6 HOH A 163 414 159 HOH HOH . F 6 HOH A 164 415 160 HOH HOH . F 6 HOH A 165 416 161 HOH HOH . F 6 HOH A 166 417 162 HOH HOH . F 6 HOH A 167 418 163 HOH HOH . F 6 HOH A 168 419 164 HOH HOH . F 6 HOH A 169 420 165 HOH HOH . F 6 HOH A 170 421 166 HOH HOH . F 6 HOH A 171 422 167 HOH HOH . F 6 HOH A 172 423 170 HOH HOH . F 6 HOH A 173 424 172 HOH HOH . F 6 HOH A 174 425 173 HOH HOH . F 6 HOH A 175 426 174 HOH HOH . F 6 HOH A 176 427 175 HOH HOH . F 6 HOH A 177 428 176 HOH HOH . F 6 HOH A 178 429 177 HOH HOH . F 6 HOH A 179 430 179 HOH HOH . F 6 HOH A 180 431 180 HOH HOH . F 6 HOH A 181 432 181 HOH HOH . F 6 HOH A 182 433 182 HOH HOH . F 6 HOH A 183 434 183 HOH HOH . F 6 HOH A 184 435 184 HOH HOH . F 6 HOH A 185 436 185 HOH HOH . F 6 HOH A 186 437 186 HOH HOH . F 6 HOH A 187 438 187 HOH HOH . F 6 HOH A 188 439 188 HOH HOH . F 6 HOH A 189 440 189 HOH HOH . F 6 HOH A 190 441 190 HOH HOH . F 6 HOH A 191 442 191 HOH HOH . F 6 HOH A 192 443 192 HOH HOH . F 6 HOH A 193 444 193 HOH HOH . F 6 HOH A 194 445 195 HOH HOH . F 6 HOH A 195 446 196 HOH HOH . F 6 HOH A 196 447 197 HOH HOH . F 6 HOH A 197 448 198 HOH HOH . F 6 HOH A 198 449 199 HOH HOH . F 6 HOH A 199 450 200 HOH HOH . F 6 HOH A 200 451 202 HOH HOH . F 6 HOH A 201 452 203 HOH HOH . F 6 HOH A 202 453 204 HOH HOH . F 6 HOH A 203 454 205 HOH HOH . F 6 HOH A 204 455 207 HOH HOH . F 6 HOH A 205 456 208 HOH HOH . F 6 HOH A 206 457 209 HOH HOH . F 6 HOH A 207 458 210 HOH HOH . F 6 HOH A 208 459 211 HOH HOH . F 6 HOH A 209 460 212 HOH HOH . F 6 HOH A 210 461 213 HOH HOH . F 6 HOH A 211 462 214 HOH HOH . F 6 HOH A 212 463 215 HOH HOH . F 6 HOH A 213 464 216 HOH HOH . F 6 HOH A 214 465 217 HOH HOH . F 6 HOH A 215 466 218 HOH HOH . F 6 HOH A 216 467 220 HOH HOH . F 6 HOH A 217 468 221 HOH HOH . F 6 HOH A 218 469 222 HOH HOH . F 6 HOH A 219 470 223 HOH HOH . F 6 HOH A 220 471 224 HOH HOH . F 6 HOH A 221 472 225 HOH HOH . F 6 HOH A 222 473 226 HOH HOH . F 6 HOH A 223 474 227 HOH HOH . F 6 HOH A 224 475 228 HOH HOH . F 6 HOH A 225 476 229 HOH HOH . F 6 HOH A 226 477 230 HOH HOH . F 6 HOH A 227 478 231 HOH HOH . F 6 HOH A 228 479 232 HOH HOH . F 6 HOH A 229 480 233 HOH HOH . F 6 HOH A 230 481 234 HOH HOH . F 6 HOH A 231 482 235 HOH HOH . F 6 HOH A 232 483 236 HOH HOH . F 6 HOH A 233 484 237 HOH HOH . F 6 HOH A 234 485 238 HOH HOH . F 6 HOH A 235 486 239 HOH HOH . F 6 HOH A 236 487 240 HOH HOH . F 6 HOH A 237 488 241 HOH HOH . F 6 HOH A 238 489 242 HOH HOH . F 6 HOH A 239 490 243 HOH HOH . F 6 HOH A 240 491 244 HOH HOH . F 6 HOH A 241 492 245 HOH HOH . F 6 HOH A 242 493 246 HOH HOH . F 6 HOH A 243 494 247 HOH HOH . F 6 HOH A 244 495 248 HOH HOH . F 6 HOH A 245 496 249 HOH HOH . F 6 HOH A 246 497 250 HOH HOH . F 6 HOH A 247 498 251 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 GOL . . . D 4 -18.051 3.966 -22.378 1 24.34 ? C1 GOL 250 A 1 HETATM 2 O O1 GOL . . . D 4 -17.312 5.159 -22.628 1 25.3 ? O1 GOL 250 A 1 HETATM 3 C C2 GOL . . . D 4 -18.687 3.453 -23.701 1 25.54 ? C2 GOL 250 A 1 HETATM 4 O O2 GOL . . . D 4 -17.658 3.165 -24.681 1 20.68 ? O2 GOL 250 A 1 HETATM 5 C C3 GOL . . . D 4 -19.694 4.491 -24.191 1 25.29 ? C3 GOL 250 A 1 HETATM 6 O O3 GOL . . . D 4 -20.133 4.229 -25.514 1 19.8 ? O3 GOL 250 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 210 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #