data_1B3W # _model_server_result.job_id TKHyiPT9wNzuulQqN9G6vw _model_server_result.datetime_utc '2024-12-26 14:50:13' _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 1b3w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":507}' # _entry.id 1B3W # _exptl.entry_id 1B3W _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 150.13 _entity.id 3 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description beta-D-xylopyranose _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 1B3W _cell.length_a 81.12 _cell.length_b 81.12 _cell.length_c 113.6 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1B3W _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _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,D _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 3 _struct_asym.id C _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 XYS _pdbx_entity_branch_link.comp_id_2 XYP _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 XYP 1 B 1 XYP B 506 XYS 2 n B XYS 2 B 2 XYS B 505 XYS # 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 disulf ? disulf1 A SG CYS 256 A CYS 256 1_555 A SG CYS 262 A CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A C PCA 1 A PCA 1 1_555 A N ALA 2 A ALA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 B O4 XYP . B XYP 1 1_555 B C1 XYS . B XYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? # _chem_comp.formula 'C5 H10 O5' _chem_comp.formula_weight 150.13 _chem_comp.id XYP _chem_comp.mon_nstd_flag . _chem_comp.name beta-D-xylopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms beta-D-xylose;D-xylose;xylose # 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 O1 C1 XYP sing 392 n n O1 HO1 XYP sing 393 n n C1 C2 XYP sing 394 n n C1 O5 XYP sing 395 n n C1 H1 XYP sing 396 n n C2 C3 XYP sing 397 n n C2 O2 XYP sing 398 n n C2 H2 XYP sing 399 n n C3 C4 XYP sing 400 n n C3 O3 XYP sing 401 n n C3 H3 XYP sing 402 n n C4 C5 XYP sing 403 n n C4 O4 XYP sing 404 n n C4 H4 XYP sing 405 n n C5 O5 XYP sing 406 n n C5 H51 XYP sing 407 n n C5 H52 XYP sing 408 n n O2 HO2 XYP sing 409 n n O3 HO3 XYP sing 410 n n O4 HO4 XYP sing 411 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 XYP DXylpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 XYP b-D-xylopyranose 'COMMON NAME' GMML 1 XYP b-D-Xylp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 XYP Xyl 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 1B3W _atom_sites.fract_transf_matrix[1][1] 0.012327 _atom_sites.fract_transf_matrix[1][2] 0.007117 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014234 _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] 0.008803 _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 XYP A 1 507 507 XYP XYS . D 4 HOH A 1 303 303 HOH HOH . D 4 HOH A 2 304 304 HOH HOH . D 4 HOH A 3 305 305 HOH HOH . D 4 HOH A 4 306 306 HOH HOH . D 4 HOH A 5 307 307 HOH HOH . D 4 HOH A 6 308 308 HOH HOH . D 4 HOH A 7 309 309 HOH HOH . D 4 HOH A 8 310 310 HOH HOH . D 4 HOH A 9 311 311 HOH HOH . D 4 HOH A 10 312 312 HOH HOH . D 4 HOH A 11 313 313 HOH HOH . D 4 HOH A 12 314 314 HOH HOH . D 4 HOH A 13 315 315 HOH HOH . D 4 HOH A 14 316 316 HOH HOH . D 4 HOH A 15 317 317 HOH HOH . D 4 HOH A 16 318 318 HOH HOH . D 4 HOH A 17 319 319 HOH HOH . D 4 HOH A 18 320 320 HOH HOH . D 4 HOH A 19 321 321 HOH HOH . D 4 HOH A 20 322 322 HOH HOH . D 4 HOH A 21 323 323 HOH HOH . D 4 HOH A 22 324 324 HOH HOH . D 4 HOH A 23 325 325 HOH HOH . D 4 HOH A 24 326 326 HOH HOH . D 4 HOH A 25 327 327 HOH HOH . D 4 HOH A 26 328 328 HOH HOH . D 4 HOH A 27 329 329 HOH HOH . D 4 HOH A 28 330 330 HOH HOH . D 4 HOH A 29 331 331 HOH HOH . D 4 HOH A 30 332 332 HOH HOH . D 4 HOH A 31 333 333 HOH HOH . D 4 HOH A 32 334 334 HOH HOH . D 4 HOH A 33 335 335 HOH HOH . D 4 HOH A 34 336 336 HOH HOH . D 4 HOH A 35 337 337 HOH HOH . D 4 HOH A 36 338 338 HOH HOH . D 4 HOH A 37 339 339 HOH HOH . D 4 HOH A 38 340 340 HOH HOH . D 4 HOH A 39 341 341 HOH HOH . D 4 HOH A 40 342 342 HOH HOH . D 4 HOH A 41 343 343 HOH HOH . D 4 HOH A 42 344 344 HOH HOH . D 4 HOH A 43 345 345 HOH HOH . D 4 HOH A 44 346 346 HOH HOH . D 4 HOH A 45 347 347 HOH HOH . D 4 HOH A 46 348 348 HOH HOH . D 4 HOH A 47 349 349 HOH HOH . D 4 HOH A 48 350 350 HOH HOH . D 4 HOH A 49 351 351 HOH HOH . D 4 HOH A 50 352 352 HOH HOH . D 4 HOH A 51 353 353 HOH HOH . D 4 HOH A 52 354 354 HOH HOH . D 4 HOH A 53 355 355 HOH HOH . D 4 HOH A 54 356 356 HOH HOH . D 4 HOH A 55 357 357 HOH HOH . D 4 HOH A 56 358 358 HOH HOH . D 4 HOH A 57 359 359 HOH HOH . D 4 HOH A 58 360 360 HOH HOH . D 4 HOH A 59 361 361 HOH HOH . D 4 HOH A 60 362 362 HOH HOH . D 4 HOH A 61 363 363 HOH HOH . D 4 HOH A 62 364 364 HOH HOH . D 4 HOH A 63 365 365 HOH HOH . D 4 HOH A 64 366 366 HOH HOH . D 4 HOH A 65 367 367 HOH HOH . D 4 HOH A 66 368 368 HOH HOH . D 4 HOH A 67 369 369 HOH HOH . D 4 HOH A 68 370 370 HOH HOH . D 4 HOH A 69 371 371 HOH HOH . D 4 HOH A 70 372 372 HOH HOH . D 4 HOH A 71 373 373 HOH HOH . D 4 HOH A 72 374 374 HOH HOH . D 4 HOH A 73 375 375 HOH HOH . D 4 HOH A 74 376 376 HOH HOH . D 4 HOH A 75 377 377 HOH HOH . D 4 HOH A 76 378 378 HOH HOH . D 4 HOH A 77 379 379 HOH HOH . D 4 HOH A 78 380 380 HOH HOH . D 4 HOH A 79 381 381 HOH HOH . D 4 HOH A 80 382 382 HOH HOH . D 4 HOH A 81 383 383 HOH HOH . D 4 HOH A 82 384 384 HOH HOH . D 4 HOH A 83 385 385 HOH HOH . D 4 HOH A 84 386 386 HOH HOH . D 4 HOH A 85 387 387 HOH HOH . D 4 HOH A 86 388 388 HOH HOH . D 4 HOH A 87 389 389 HOH HOH . D 4 HOH A 88 390 390 HOH HOH . D 4 HOH A 89 391 391 HOH HOH . D 4 HOH A 90 392 392 HOH HOH . D 4 HOH A 91 393 393 HOH HOH . D 4 HOH A 92 394 394 HOH HOH . D 4 HOH A 93 395 395 HOH HOH . D 4 HOH A 94 396 396 HOH HOH . D 4 HOH A 95 397 397 HOH HOH . D 4 HOH A 96 398 398 HOH HOH . D 4 HOH A 97 399 399 HOH HOH . D 4 HOH A 98 400 400 HOH HOH . D 4 HOH A 99 401 401 HOH HOH . D 4 HOH A 100 402 402 HOH HOH . D 4 HOH A 101 403 403 HOH HOH . D 4 HOH A 102 404 404 HOH HOH . D 4 HOH A 103 405 405 HOH HOH . D 4 HOH A 104 406 406 HOH HOH . D 4 HOH A 105 407 407 HOH HOH . D 4 HOH A 106 408 408 HOH HOH . D 4 HOH A 107 409 409 HOH HOH . D 4 HOH A 108 410 410 HOH HOH . D 4 HOH A 109 411 411 HOH HOH . D 4 HOH A 110 412 412 HOH HOH . D 4 HOH A 111 413 413 HOH HOH . D 4 HOH A 112 414 414 HOH HOH . D 4 HOH A 113 415 415 HOH HOH . D 4 HOH A 114 416 416 HOH HOH . D 4 HOH A 115 417 417 HOH HOH . D 4 HOH A 116 418 418 HOH HOH . D 4 HOH A 117 419 419 HOH HOH . D 4 HOH A 118 420 420 HOH HOH . D 4 HOH A 119 421 421 HOH HOH . D 4 HOH A 120 422 422 HOH HOH . D 4 HOH A 121 423 423 HOH HOH . D 4 HOH A 122 424 424 HOH HOH . D 4 HOH A 123 425 425 HOH HOH . D 4 HOH A 124 426 426 HOH HOH . D 4 HOH A 125 427 427 HOH HOH . D 4 HOH A 126 428 428 HOH HOH . D 4 HOH A 127 429 429 HOH HOH . D 4 HOH A 128 430 430 HOH HOH . D 4 HOH A 129 431 431 HOH HOH . D 4 HOH A 130 432 432 HOH HOH . D 4 HOH A 131 433 433 HOH HOH . D 4 HOH A 132 434 434 HOH HOH . D 4 HOH A 133 435 435 HOH HOH . D 4 HOH A 134 436 436 HOH HOH . D 4 HOH A 135 437 437 HOH HOH . D 4 HOH A 136 438 438 HOH HOH . D 4 HOH A 137 439 439 HOH HOH . D 4 HOH A 138 440 440 HOH HOH . D 4 HOH A 139 441 441 HOH HOH . D 4 HOH A 140 442 442 HOH HOH . D 4 HOH A 141 443 443 HOH HOH . D 4 HOH A 142 444 444 HOH HOH . D 4 HOH A 143 445 445 HOH HOH . D 4 HOH A 144 446 446 HOH HOH . D 4 HOH A 145 447 447 HOH HOH . D 4 HOH A 146 448 448 HOH HOH . D 4 HOH A 147 449 449 HOH HOH . D 4 HOH A 148 450 450 HOH HOH . D 4 HOH A 149 451 451 HOH HOH . D 4 HOH A 150 452 452 HOH HOH . D 4 HOH A 151 453 453 HOH HOH . D 4 HOH A 152 454 454 HOH HOH . D 4 HOH A 153 455 455 HOH HOH . D 4 HOH A 154 456 456 HOH HOH . D 4 HOH A 155 457 457 HOH HOH . D 4 HOH A 156 458 458 HOH HOH . D 4 HOH A 157 459 459 HOH HOH . D 4 HOH A 158 460 460 HOH HOH . D 4 HOH A 159 461 461 HOH HOH . D 4 HOH A 160 462 462 HOH HOH . D 4 HOH A 161 463 463 HOH HOH . D 4 HOH A 162 464 464 HOH HOH . D 4 HOH A 163 465 465 HOH HOH . D 4 HOH A 164 466 466 HOH HOH . D 4 HOH A 165 467 467 HOH HOH . D 4 HOH A 166 468 468 HOH HOH . D 4 HOH A 167 469 469 HOH HOH . D 4 HOH A 168 470 470 HOH HOH . D 4 HOH A 169 471 471 HOH HOH . D 4 HOH A 170 472 472 HOH HOH . D 4 HOH A 171 473 473 HOH HOH . D 4 HOH A 172 474 474 HOH HOH . D 4 HOH A 173 475 475 HOH HOH . D 4 HOH A 174 476 476 HOH HOH . D 4 HOH A 175 477 477 HOH HOH . D 4 HOH A 176 478 478 HOH HOH . D 4 HOH A 177 479 479 HOH HOH . D 4 HOH A 178 480 480 HOH HOH . D 4 HOH A 179 481 481 HOH HOH . D 4 HOH A 180 482 482 HOH HOH . D 4 HOH A 181 483 483 HOH HOH . D 4 HOH A 182 484 484 HOH HOH . D 4 HOH A 183 485 485 HOH HOH . D 4 HOH A 184 486 486 HOH HOH . D 4 HOH A 185 487 487 HOH HOH . D 4 HOH A 186 488 488 HOH HOH . D 4 HOH A 187 489 489 HOH HOH . D 4 HOH A 188 490 490 HOH HOH . D 4 HOH A 189 491 491 HOH HOH . D 4 HOH A 190 492 492 HOH HOH . D 4 HOH A 191 493 493 HOH HOH . D 4 HOH A 192 494 494 HOH HOH . D 4 HOH A 193 495 495 HOH HOH . D 4 HOH A 194 496 496 HOH HOH . D 4 HOH A 195 497 497 HOH HOH . D 4 HOH A 196 498 498 HOH HOH . D 4 HOH A 197 499 499 HOH HOH . D 4 HOH A 198 500 500 HOH HOH . D 4 HOH A 199 501 501 HOH HOH . D 4 HOH A 200 502 502 HOH HOH . D 4 HOH A 201 503 503 HOH HOH . D 4 HOH A 202 504 504 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 O O1 XYP . . . C 3 90.693 62.156 21.331 1 25.92 ? O1 XYP 507 A 1 HETATM 2 C C1 XYP . . . C 3 91.109 62 20.018 1 28.42 ? C1 XYP 507 A 1 HETATM 3 C C2 XYP . . . C 3 90.099 62.656 19.069 1 27.78 ? C2 XYP 507 A 1 HETATM 4 C C3 XYP . . . C 3 90.597 62.539 17.633 1 27.4 ? C3 XYP 507 A 1 HETATM 5 C C4 XYP . . . C 3 91.999 63.158 17.517 1 28.47 ? C4 XYP 507 A 1 HETATM 6 C C5 XYP . . . C 3 92.938 62.522 18.551 1 27.25 ? C5 XYP 507 A 1 HETATM 7 O O2 XYP . . . C 3 88.842 62.002 19.18 1 28.8 ? O2 XYP 507 A 1 HETATM 8 O O3 XYP . . . C 3 89.687 63.203 16.762 1 29.58 ? O3 XYP 507 A 1 HETATM 9 O O4 XYP . . . C 3 92.519 62.943 16.211 1 30.61 ? O4 XYP 507 A 1 HETATM 10 O O5 XYP . . . C 3 92.395 62.629 19.891 1 28.35 ? O5 XYP 507 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 10 #