data_1DBP # _model_server_result.job_id WUCvVmvgZthc-wcyfG3flw _model_server_result.datetime_utc '2024-11-27 03:03:12' _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 1dbp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":272}' # _entry.id 1DBP # _exptl.entry_id 1DBP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.13 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description beta-D-ribopyranose _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 1DBP _cell.length_a 74.84 _cell.length_b 88.88 _cell.length_c 39.86 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DBP _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 'C5 H10 O5' _chem_comp.formula_weight 150.13 _chem_comp.id RIP _chem_comp.mon_nstd_flag . _chem_comp.name beta-D-ribopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms 'beta-D-ribose;D-ribose;ribose;RIBOSE(PYRANOSE FORM)' # 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 RIP sing 264 n n C1 O1 RIP sing 265 n n C1 O5 RIP sing 266 n n C1 H1 RIP sing 267 n n C2 C3 RIP sing 268 n n C2 O2 RIP sing 269 n n C2 H2 RIP sing 270 n n C3 C4 RIP sing 271 n n C3 O3 RIP sing 272 n n C3 H3 RIP sing 273 n n C4 C5 RIP sing 274 n n C4 O4 RIP sing 275 n n C4 H4 RIP sing 276 n n C5 O5 RIP sing 277 n n C5 H51 RIP sing 278 n n C5 H52 RIP sing 279 n n O1 HO1 RIP sing 280 n n O2 HO2 RIP sing 281 n n O3 HO3 RIP sing 282 n n O4 HO4 RIP sing 283 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version RIP DRibpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 RIP b-D-ribopyranose 'COMMON NAME' GMML 1 RIP b-D-Ribp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 RIP Rib 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 1DBP _atom_sites.fract_transf_matrix[1][1] 0.013362 _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] 0.011251 _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] 0.025088 _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 RIP A 1 272 1 RIP RIP . C 3 HOH A 1 273 1 HOH HOH . C 3 HOH A 2 274 2 HOH HOH . C 3 HOH A 3 275 4 HOH HOH . C 3 HOH A 4 276 5 HOH HOH . C 3 HOH A 5 277 6 HOH HOH . C 3 HOH A 6 278 7 HOH HOH . C 3 HOH A 7 279 8 HOH HOH . C 3 HOH A 8 280 9 HOH HOH . C 3 HOH A 9 281 10 HOH HOH . C 3 HOH A 10 282 11 HOH HOH . C 3 HOH A 11 283 13 HOH HOH . C 3 HOH A 12 284 14 HOH HOH . C 3 HOH A 13 285 15 HOH HOH . C 3 HOH A 14 286 16 HOH HOH . C 3 HOH A 15 287 17 HOH HOH . C 3 HOH A 16 288 18 HOH HOH . C 3 HOH A 17 289 19 HOH HOH . C 3 HOH A 18 290 20 HOH HOH . C 3 HOH A 19 291 21 HOH HOH . C 3 HOH A 20 292 22 HOH HOH . C 3 HOH A 21 293 23 HOH HOH . C 3 HOH A 22 294 24 HOH HOH . C 3 HOH A 23 295 25 HOH HOH . C 3 HOH A 24 296 26 HOH HOH . C 3 HOH A 25 297 27 HOH HOH . C 3 HOH A 26 298 28 HOH HOH . C 3 HOH A 27 299 30 HOH HOH . C 3 HOH A 28 300 31 HOH HOH . C 3 HOH A 29 301 32 HOH HOH . C 3 HOH A 30 302 33 HOH HOH . C 3 HOH A 31 303 34 HOH HOH . C 3 HOH A 32 304 36 HOH HOH . C 3 HOH A 33 305 38 HOH HOH . C 3 HOH A 34 306 39 HOH HOH . C 3 HOH A 35 307 40 HOH HOH . C 3 HOH A 36 308 41 HOH HOH . C 3 HOH A 37 309 42 HOH HOH . C 3 HOH A 38 310 43 HOH HOH . C 3 HOH A 39 311 46 HOH HOH . C 3 HOH A 40 312 48 HOH HOH . C 3 HOH A 41 313 49 HOH HOH . C 3 HOH A 42 314 50 HOH HOH . C 3 HOH A 43 315 52 HOH HOH . C 3 HOH A 44 316 53 HOH HOH . C 3 HOH A 45 317 54 HOH HOH . C 3 HOH A 46 318 55 HOH HOH . C 3 HOH A 47 319 56 HOH HOH . C 3 HOH A 48 320 59 HOH HOH . C 3 HOH A 49 321 60 HOH HOH . C 3 HOH A 50 322 61 HOH HOH . C 3 HOH A 51 323 63 HOH HOH . C 3 HOH A 52 324 65 HOH HOH . C 3 HOH A 53 325 66 HOH HOH . C 3 HOH A 54 326 67 HOH HOH . C 3 HOH A 55 327 68 HOH HOH . C 3 HOH A 56 328 69 HOH HOH . C 3 HOH A 57 329 71 HOH HOH . C 3 HOH A 58 330 72 HOH HOH . C 3 HOH A 59 331 73 HOH HOH . C 3 HOH A 60 332 74 HOH HOH . C 3 HOH A 61 333 75 HOH HOH . C 3 HOH A 62 334 76 HOH HOH . C 3 HOH A 63 335 77 HOH HOH . C 3 HOH A 64 336 78 HOH HOH . C 3 HOH A 65 337 80 HOH HOH . C 3 HOH A 66 338 81 HOH HOH . C 3 HOH A 67 339 82 HOH HOH . C 3 HOH A 68 340 83 HOH HOH . C 3 HOH A 69 341 84 HOH HOH . C 3 HOH A 70 342 85 HOH HOH . C 3 HOH A 71 343 87 HOH HOH . C 3 HOH A 72 344 88 HOH HOH . C 3 HOH A 73 345 90 HOH HOH . C 3 HOH A 74 346 91 HOH HOH . C 3 HOH A 75 347 93 HOH HOH . C 3 HOH A 76 348 95 HOH HOH . C 3 HOH A 77 349 97 HOH HOH . C 3 HOH A 78 350 98 HOH HOH . C 3 HOH A 79 351 99 HOH HOH . C 3 HOH A 80 352 101 HOH HOH . C 3 HOH A 81 353 102 HOH HOH . C 3 HOH A 82 354 103 HOH HOH . C 3 HOH A 83 355 104 HOH HOH . C 3 HOH A 84 356 105 HOH HOH . C 3 HOH A 85 357 106 HOH HOH . C 3 HOH A 86 358 107 HOH HOH . C 3 HOH A 87 359 108 HOH HOH . C 3 HOH A 88 360 110 HOH HOH . C 3 HOH A 89 361 112 HOH HOH . C 3 HOH A 90 362 114 HOH HOH . C 3 HOH A 91 363 116 HOH HOH . C 3 HOH A 92 364 117 HOH HOH . C 3 HOH A 93 365 118 HOH HOH . C 3 HOH A 94 366 119 HOH HOH . C 3 HOH A 95 367 120 HOH HOH . C 3 HOH A 96 368 121 HOH HOH . C 3 HOH A 97 369 123 HOH HOH . C 3 HOH A 98 370 124 HOH HOH . C 3 HOH A 99 371 125 HOH HOH . C 3 HOH A 100 372 126 HOH HOH . C 3 HOH A 101 373 128 HOH HOH . C 3 HOH A 102 374 129 HOH HOH . C 3 HOH A 103 375 130 HOH HOH . C 3 HOH A 104 376 131 HOH HOH . C 3 HOH A 105 377 132 HOH HOH . C 3 HOH A 106 378 133 HOH HOH . C 3 HOH A 107 379 135 HOH HOH . C 3 HOH A 108 380 136 HOH HOH . C 3 HOH A 109 381 137 HOH HOH . C 3 HOH A 110 382 139 HOH HOH . C 3 HOH A 111 383 140 HOH HOH . C 3 HOH A 112 384 142 HOH HOH . C 3 HOH A 113 385 143 HOH HOH . C 3 HOH A 114 386 144 HOH HOH . C 3 HOH A 115 387 145 HOH HOH . C 3 HOH A 116 388 146 HOH HOH . C 3 HOH A 117 389 147 HOH HOH . C 3 HOH A 118 390 149 HOH HOH . C 3 HOH A 119 391 150 HOH HOH . C 3 HOH A 120 392 152 HOH HOH . C 3 HOH A 121 393 153 HOH HOH . C 3 HOH A 122 394 154 HOH HOH . C 3 HOH A 123 395 155 HOH HOH . C 3 HOH A 124 396 156 HOH HOH . C 3 HOH A 125 397 157 HOH HOH . C 3 HOH A 126 398 158 HOH HOH . C 3 HOH A 127 399 160 HOH HOH . C 3 HOH A 128 400 161 HOH HOH . C 3 HOH A 129 401 163 HOH HOH . C 3 HOH A 130 402 164 HOH HOH . C 3 HOH A 131 403 165 HOH HOH . C 3 HOH A 132 404 166 HOH HOH . C 3 HOH A 133 405 167 HOH HOH . C 3 HOH A 134 406 168 HOH HOH . C 3 HOH A 135 407 170 HOH HOH . C 3 HOH A 136 408 171 HOH HOH . C 3 HOH A 137 409 173 HOH HOH . C 3 HOH A 138 410 174 HOH HOH . C 3 HOH A 139 411 176 HOH HOH . C 3 HOH A 140 412 178 HOH HOH . C 3 HOH A 141 413 180 HOH HOH . C 3 HOH A 142 414 182 HOH HOH . C 3 HOH A 143 415 183 HOH HOH . C 3 HOH A 144 416 185 HOH HOH . C 3 HOH A 145 417 186 HOH HOH . C 3 HOH A 146 418 188 HOH HOH . C 3 HOH A 147 419 190 HOH HOH . C 3 HOH A 148 420 191 HOH HOH . C 3 HOH A 149 421 192 HOH HOH . C 3 HOH A 150 422 195 HOH HOH . C 3 HOH A 151 423 196 HOH HOH . C 3 HOH A 152 424 197 HOH HOH . C 3 HOH A 153 425 198 HOH HOH . C 3 HOH A 154 426 199 HOH HOH . C 3 HOH A 155 427 200 HOH HOH . C 3 HOH A 156 428 201 HOH HOH . C 3 HOH A 157 429 202 HOH HOH . C 3 HOH A 158 430 205 HOH HOH . C 3 HOH A 159 431 206 HOH HOH . C 3 HOH A 160 432 207 HOH HOH . C 3 HOH A 161 433 209 HOH HOH . C 3 HOH A 162 434 210 HOH HOH . C 3 HOH A 163 435 212 HOH HOH . C 3 HOH A 164 436 213 HOH HOH . C 3 HOH A 165 437 215 HOH HOH . C 3 HOH A 166 438 220 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 RIP . . . B 2 50.014 33.551 43.735 1 14.05 ? C1 RIP 272 A 1 HETATM 2 C C2 RIP . . . B 2 49.354 32.982 44.978 1 13.71 ? C2 RIP 272 A 1 HETATM 3 C C3 RIP . . . B 2 49.012 34.11 45.94 1 18.56 ? C3 RIP 272 A 1 HETATM 4 C C4 RIP . . . B 2 50.27 34.93 46.252 1 12.53 ? C4 RIP 272 A 1 HETATM 5 C C5 RIP . . . B 2 50.932 35.399 44.972 1 11.32 ? C5 RIP 272 A 1 HETATM 6 O O1 RIP . . . B 2 50.359 32.514 42.847 1 13.3 ? O1 RIP 272 A 1 HETATM 7 O O2 RIP . . . B 2 48.175 32.297 44.62 1 16.03 ? O2 RIP 272 A 1 HETATM 8 O O3 RIP . . . B 2 48.006 34.937 45.362 1 17.4 ? O3 RIP 272 A 1 HETATM 9 O O4 RIP . . . B 2 49.938 36.045 47.031 1 17.27 ? O4 RIP 272 A 1 HETATM 10 O O5 RIP . . . B 2 51.178 34.296 44.099 1 18.66 ? O5 RIP 272 A 1 HETATM 11 H H1 RIP . . . B 2 49.325 34.245 43.227 1 0 ? H1 RIP 272 A 1 HETATM 12 H H2 RIP . . . B 2 50.054 32.295 45.471 1 0 ? H2 RIP 272 A 1 HETATM 13 H H3 RIP . . . B 2 48.635 33.675 46.872 1 0 ? H3 RIP 272 A 1 HETATM 14 H H4 RIP . . . B 2 50.978 34.294 46.801 1 0 ? H4 RIP 272 A 1 HETATM 15 H H51 RIP . . . B 2 51.893 35.883 45.199 1 0 ? H51 RIP 272 A 1 HETATM 16 H H52 RIP . . . B 2 50.283 36.117 44.454 1 0 ? H52 RIP 272 A 1 HETATM 17 H HO1 RIP . . . B 2 49.604 31.933 42.728 1 0 ? HO1 RIP 272 A 1 HETATM 18 H HO2 RIP . . . B 2 47.904 32.573 43.742 1 0 ? HO2 RIP 272 A 1 HETATM 19 H HO3 RIP . . . B 2 47.917 35.739 45.881 1 0 ? HO3 RIP 272 A 1 HETATM 20 H HO4 RIP . . . B 2 49.765 35.763 47.932 1 0 ? HO4 RIP 272 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #