data_5W8E # _model_server_result.job_id czDYepyUyecCj3kG68aMsA _model_server_result.datetime_utc '2024-11-15 00:28:21' _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 5w8e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5W8E # _exptl.entry_id 5W8E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 468.527 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-4-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)-2-[(3-methylbutanoyl)amino]butanoic acid' _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 5W8E _cell.length_a 91.27 _cell.length_b 91.27 _cell.length_c 98.12 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5W8E _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C19 H28 N6 O6 S' _chem_comp.formula_weight 468.527 _chem_comp.id SXZ _chem_comp.mon_nstd_flag . _chem_comp.name '(2S)-4-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)-2-[(3-methylbutanoyl)amino]butanoic 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 C9 C7 SXZ sing 319 n n C10 C7 SXZ sing 320 n n C7 C3 SXZ sing 321 n n C3 C1 SXZ sing 322 n n C1 O2 SXZ doub 323 n n C1 N SXZ sing 324 n n N CA SXZ sing 325 n n OXT C SXZ doub 326 n n CA C SXZ sing 327 n n CA CB SXZ sing 328 n n C O SXZ sing 329 n n CG CB SXZ sing 330 n n CG SD SXZ sing 331 n n SD C5' SXZ sing 332 n n C5' C4' SXZ sing 333 n n O4' C4' SXZ sing 334 n n O4' C1' SXZ sing 335 n n C4' C3' SXZ sing 336 n n C8 N7 SXZ doub 337 n y C8 N9 SXZ sing 338 n y N7 C5 SXZ sing 339 n y N9 C1' SXZ sing 340 n n N9 C4 SXZ sing 341 n y C3' C2' SXZ sing 342 n n C3' O3' SXZ sing 343 n n C1' C2' SXZ sing 344 n n C5 C4 SXZ doub 345 n y C5 C6 SXZ sing 346 n y N6 C6 SXZ sing 347 n n C2' O2' SXZ sing 348 n n C4 N3 SXZ sing 349 n y C6 N1 SXZ doub 350 n y N3 C2 SXZ doub 351 n y N1 C2 SXZ sing 352 n y O H1 SXZ sing 353 n n CA H2 SXZ sing 354 n n N H3 SXZ sing 355 n n CB H4 SXZ sing 356 n n CB H5 SXZ sing 357 n n CG H6 SXZ sing 358 n n CG H7 SXZ sing 359 n n C5' H8 SXZ sing 360 n n C5' H9 SXZ sing 361 n n C4' H10 SXZ sing 362 n n C1' H11 SXZ sing 363 n n C2' H12 SXZ sing 364 n n O2' H13 SXZ sing 365 n n C3' H14 SXZ sing 366 n n O3' H15 SXZ sing 367 n n C8 H16 SXZ sing 368 n n N6 H17 SXZ sing 369 n n N6 H18 SXZ sing 370 n n C2 H19 SXZ sing 371 n n C3 H20 SXZ sing 372 n n C3 H21 SXZ sing 373 n n C7 H22 SXZ sing 374 n n C9 H23 SXZ sing 375 n n C9 H24 SXZ sing 376 n n C9 H25 SXZ sing 377 n n C10 H26 SXZ sing 378 n n C10 H27 SXZ sing 379 n n C10 H28 SXZ sing 380 n n # _atom_sites.entry_id 5W8E _atom_sites.fract_transf_matrix[1][1] 0.010957 _atom_sites.fract_transf_matrix[1][2] 0.006326 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012651 _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] 0.010192 _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 SXZ A 1 301 301 SXZ SXZ . C 3 CL A 1 302 302 CL CL . D 4 GOL A 1 303 303 GOL GOL . E 5 ADE A 1 304 400 ADE ADE . F 6 HOH A 1 401 188 HOH HOH . F 6 HOH A 2 402 137 HOH HOH . F 6 HOH A 3 403 19 HOH HOH . F 6 HOH A 4 404 145 HOH HOH . F 6 HOH A 5 405 122 HOH HOH . F 6 HOH A 6 406 186 HOH HOH . F 6 HOH A 7 407 4 HOH HOH . F 6 HOH A 8 408 107 HOH HOH . F 6 HOH A 9 409 146 HOH HOH . F 6 HOH A 10 410 74 HOH HOH . F 6 HOH A 11 411 134 HOH HOH . F 6 HOH A 12 412 23 HOH HOH . F 6 HOH A 13 413 87 HOH HOH . F 6 HOH A 14 414 3 HOH HOH . F 6 HOH A 15 415 83 HOH HOH . F 6 HOH A 16 416 95 HOH HOH . F 6 HOH A 17 417 79 HOH HOH . F 6 HOH A 18 418 49 HOH HOH . F 6 HOH A 19 419 33 HOH HOH . F 6 HOH A 20 420 60 HOH HOH . F 6 HOH A 21 421 114 HOH HOH . F 6 HOH A 22 422 69 HOH HOH . F 6 HOH A 23 423 150 HOH HOH . F 6 HOH A 24 424 142 HOH HOH . F 6 HOH A 25 425 46 HOH HOH . F 6 HOH A 26 426 64 HOH HOH . F 6 HOH A 27 427 73 HOH HOH . F 6 HOH A 28 428 51 HOH HOH . F 6 HOH A 29 429 28 HOH HOH . F 6 HOH A 30 430 81 HOH HOH . F 6 HOH A 31 431 26 HOH HOH . F 6 HOH A 32 432 135 HOH HOH . F 6 HOH A 33 433 54 HOH HOH . F 6 HOH A 34 434 136 HOH HOH . F 6 HOH A 35 435 131 HOH HOH . F 6 HOH A 36 436 37 HOH HOH . F 6 HOH A 37 437 9 HOH HOH . F 6 HOH A 38 438 94 HOH HOH . F 6 HOH A 39 439 43 HOH HOH . F 6 HOH A 40 440 52 HOH HOH . F 6 HOH A 41 441 38 HOH HOH . F 6 HOH A 42 442 21 HOH HOH . F 6 HOH A 43 443 48 HOH HOH . F 6 HOH A 44 444 109 HOH HOH . F 6 HOH A 45 445 100 HOH HOH . F 6 HOH A 46 446 13 HOH HOH . F 6 HOH A 47 447 40 HOH HOH . F 6 HOH A 48 448 103 HOH HOH . F 6 HOH A 49 449 159 HOH HOH . F 6 HOH A 50 450 2 HOH HOH . F 6 HOH A 51 451 50 HOH HOH . F 6 HOH A 52 452 44 HOH HOH . F 6 HOH A 53 453 189 HOH HOH . F 6 HOH A 54 454 68 HOH HOH . F 6 HOH A 55 455 30 HOH HOH . F 6 HOH A 56 456 112 HOH HOH . F 6 HOH A 57 457 182 HOH HOH . F 6 HOH A 58 458 139 HOH HOH . F 6 HOH A 59 459 88 HOH HOH . F 6 HOH A 60 460 163 HOH HOH . F 6 HOH A 61 461 59 HOH HOH . F 6 HOH A 62 462 16 HOH HOH . F 6 HOH A 63 463 36 HOH HOH . F 6 HOH A 64 464 86 HOH HOH . F 6 HOH A 65 465 53 HOH HOH . F 6 HOH A 66 466 106 HOH HOH . F 6 HOH A 67 467 125 HOH HOH . F 6 HOH A 68 468 192 HOH HOH . F 6 HOH A 69 469 34 HOH HOH . F 6 HOH A 70 470 156 HOH HOH . F 6 HOH A 71 471 233 HOH HOH . F 6 HOH A 72 472 14 HOH HOH . F 6 HOH A 73 473 113 HOH HOH . F 6 HOH A 74 474 35 HOH HOH . F 6 HOH A 75 475 199 HOH HOH . F 6 HOH A 76 476 170 HOH HOH . F 6 HOH A 77 477 63 HOH HOH . F 6 HOH A 78 478 104 HOH HOH . F 6 HOH A 79 479 193 HOH HOH . F 6 HOH A 80 480 144 HOH HOH . F 6 HOH A 81 481 154 HOH HOH . F 6 HOH A 82 482 152 HOH HOH . F 6 HOH A 83 483 284 HOH HOH . F 6 HOH A 84 484 78 HOH HOH . F 6 HOH A 85 485 155 HOH HOH . F 6 HOH A 86 486 102 HOH HOH . F 6 HOH A 87 487 12 HOH HOH . F 6 HOH A 88 488 55 HOH HOH . F 6 HOH A 89 489 82 HOH HOH . F 6 HOH A 90 490 77 HOH HOH . F 6 HOH A 91 491 232 HOH HOH . F 6 HOH A 92 492 31 HOH HOH . F 6 HOH A 93 493 167 HOH HOH . F 6 HOH A 94 494 108 HOH HOH . F 6 HOH A 95 495 148 HOH HOH . F 6 HOH A 96 496 66 HOH HOH . F 6 HOH A 97 497 47 HOH HOH . F 6 HOH A 98 498 128 HOH HOH . F 6 HOH A 99 499 176 HOH HOH . F 6 HOH A 100 500 179 HOH HOH . F 6 HOH A 101 501 45 HOH HOH . F 6 HOH A 102 502 1 HOH HOH . F 6 HOH A 103 503 39 HOH HOH . F 6 HOH A 104 504 126 HOH HOH . F 6 HOH A 105 505 292 HOH HOH . F 6 HOH A 106 506 124 HOH HOH . F 6 HOH A 107 507 29 HOH HOH . F 6 HOH A 108 508 200 HOH HOH . F 6 HOH A 109 509 217 HOH HOH . F 6 HOH A 110 510 169 HOH HOH . F 6 HOH A 111 511 165 HOH HOH . F 6 HOH A 112 512 209 HOH HOH . F 6 HOH A 113 513 42 HOH HOH . F 6 HOH A 114 514 10 HOH HOH . F 6 HOH A 115 515 93 HOH HOH . F 6 HOH A 116 516 127 HOH HOH . F 6 HOH A 117 517 84 HOH HOH . F 6 HOH A 118 518 147 HOH HOH . F 6 HOH A 119 519 58 HOH HOH . F 6 HOH A 120 520 121 HOH HOH . F 6 HOH A 121 521 138 HOH HOH . F 6 HOH A 122 522 166 HOH HOH . F 6 HOH A 123 523 133 HOH HOH . F 6 HOH A 124 524 105 HOH HOH . F 6 HOH A 125 525 164 HOH HOH . F 6 HOH A 126 526 172 HOH HOH . F 6 HOH A 127 527 183 HOH HOH . F 6 HOH A 128 528 173 HOH HOH . F 6 HOH A 129 529 130 HOH HOH . F 6 HOH A 130 530 15 HOH HOH . F 6 HOH A 131 531 168 HOH HOH . F 6 HOH A 132 532 177 HOH HOH . F 6 HOH A 133 533 22 HOH HOH . F 6 HOH A 134 534 215 HOH HOH . F 6 HOH A 135 535 111 HOH HOH . F 6 HOH A 136 536 56 HOH HOH . F 6 HOH A 137 537 160 HOH HOH . F 6 HOH A 138 538 157 HOH HOH . F 6 HOH A 139 539 7 HOH HOH . F 6 HOH A 140 540 178 HOH HOH . F 6 HOH A 141 541 6 HOH HOH . F 6 HOH A 142 542 132 HOH HOH . F 6 HOH A 143 543 190 HOH HOH . F 6 HOH A 144 544 141 HOH HOH . F 6 HOH A 145 545 27 HOH HOH . F 6 HOH A 146 546 61 HOH HOH . F 6 HOH A 147 547 8 HOH HOH . F 6 HOH A 148 548 118 HOH HOH . F 6 HOH A 149 549 153 HOH HOH . F 6 HOH A 150 550 24 HOH HOH . F 6 HOH A 151 551 32 HOH HOH . F 6 HOH A 152 552 70 HOH HOH . F 6 HOH A 153 553 116 HOH HOH . F 6 HOH A 154 554 5 HOH HOH . F 6 HOH A 155 555 101 HOH HOH . F 6 HOH A 156 556 18 HOH HOH . F 6 HOH A 157 557 11 HOH HOH . F 6 HOH A 158 558 228 HOH HOH . F 6 HOH A 159 559 72 HOH HOH . F 6 HOH A 160 560 20 HOH HOH . F 6 HOH A 161 561 65 HOH HOH . F 6 HOH A 162 562 57 HOH HOH . F 6 HOH A 163 563 97 HOH HOH . F 6 HOH A 164 564 129 HOH HOH . F 6 HOH A 165 565 89 HOH HOH . F 6 HOH A 166 566 17 HOH HOH . F 6 HOH A 167 567 184 HOH HOH . F 6 HOH A 168 568 75 HOH HOH . F 6 HOH A 169 569 196 HOH HOH . F 6 HOH A 170 570 62 HOH HOH . F 6 HOH A 171 571 98 HOH HOH . F 6 HOH A 172 572 252 HOH HOH . F 6 HOH A 173 573 162 HOH HOH . F 6 HOH A 174 574 110 HOH HOH . F 6 HOH A 175 575 92 HOH HOH . F 6 HOH A 176 576 259 HOH HOH . F 6 HOH A 177 577 185 HOH HOH . F 6 HOH A 178 578 115 HOH HOH . F 6 HOH A 179 579 205 HOH HOH . F 6 HOH A 180 580 76 HOH HOH . F 6 HOH A 181 581 140 HOH HOH . F 6 HOH A 182 582 313 HOH HOH . F 6 HOH A 183 583 96 HOH HOH . F 6 HOH A 184 584 194 HOH HOH . F 6 HOH A 185 585 80 HOH HOH . F 6 HOH A 186 586 158 HOH HOH . F 6 HOH A 187 587 117 HOH HOH . F 6 HOH A 188 588 229 HOH HOH . F 6 HOH A 189 589 175 HOH HOH . F 6 HOH A 190 590 71 HOH HOH . F 6 HOH A 191 591 120 HOH HOH . F 6 HOH A 192 592 85 HOH HOH . F 6 HOH A 193 593 276 HOH HOH . F 6 HOH A 194 594 123 HOH HOH . F 6 HOH A 195 595 151 HOH HOH . F 6 HOH A 196 596 90 HOH HOH . F 6 HOH A 197 597 149 HOH HOH . F 6 HOH A 198 598 171 HOH HOH . F 6 HOH A 199 599 119 HOH HOH . F 6 HOH A 200 600 25 HOH HOH . F 6 HOH A 201 601 67 HOH HOH . F 6 HOH A 202 602 99 HOH HOH . F 6 HOH A 203 603 143 HOH HOH . F 6 HOH A 204 604 281 HOH HOH . F 6 HOH A 205 605 174 HOH HOH . F 6 HOH A 206 606 41 HOH HOH . F 6 HOH A 207 607 275 HOH HOH . F 6 HOH A 208 608 208 HOH HOH . F 6 HOH A 209 609 161 HOH HOH . F 6 HOH A 210 610 91 HOH HOH . F 6 HOH A 211 611 211 HOH HOH . F 6 HOH A 212 612 180 HOH HOH . F 6 HOH A 213 613 204 HOH HOH . F 6 HOH A 214 614 181 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 OXT SXZ . . . B 2 -33.6 27.767 -10.75 1 26.91 ? OXT SXZ 301 A 1 HETATM 2 C C SXZ . . . B 2 -32.866 26.794 -10.461 1 26.28 ? C SXZ 301 A 1 HETATM 3 O O SXZ . . . B 2 -33.328 25.737 -9.975 1 27.19 ? O SXZ 301 A 1 HETATM 4 C CA SXZ . . . B 2 -31.385 26.907 -10.705 1 25.49 ? CA SXZ 301 A 1 HETATM 5 N N SXZ . . . B 2 -31.071 27.282 -12.085 1 24.07 ? N SXZ 301 A 1 HETATM 6 C CB SXZ . . . B 2 -30.827 28.007 -9.788 1 25.87 ? CB SXZ 301 A 1 HETATM 7 C CG SXZ . . . B 2 -29.358 28.366 -10.013 1 26.54 ? CG SXZ 301 A 1 HETATM 8 S SD SXZ . . . B 2 -28.812 29.445 -8.719 1 27.66 ? SD SXZ 301 A 1 HETATM 9 C C5' SXZ . . . B 2 -28.48 28.434 -7.306 1 28.14 ? C5' SXZ 301 A 1 HETATM 10 C C4' SXZ . . . B 2 -28.933 29.108 -6.018 1 28.46 ? C4' SXZ 301 A 1 HETATM 11 O O4' SXZ . . . B 2 -30.353 29.289 -6.026 1 29.01 ? O4' SXZ 301 A 1 HETATM 12 C C1' SXZ . . . B 2 -30.881 28.963 -4.74 1 28.06 ? C1' SXZ 301 A 1 HETATM 13 C C2' SXZ . . . B 2 -29.964 27.863 -4.225 1 28.6 ? C2' SXZ 301 A 1 HETATM 14 O O2' SXZ . . . B 2 -29.932 27.816 -2.795 1 29.07 ? O2' SXZ 301 A 1 HETATM 15 C C3' SXZ . . . B 2 -28.614 28.255 -4.795 1 28.21 ? C3' SXZ 301 A 1 HETATM 16 O O3' SXZ . . . B 2 -27.889 29.054 -3.851 1 28.7 ? O3' SXZ 301 A 1 HETATM 17 N N9 SXZ . . . B 2 -32.302 28.546 -4.848 1 26.44 ? N9 SXZ 301 A 1 HETATM 18 C C8 SXZ . . . B 2 -32.819 27.609 -5.666 1 26.43 ? C8 SXZ 301 A 1 HETATM 19 N N7 SXZ . . . B 2 -34.157 27.539 -5.465 1 26.45 ? N7 SXZ 301 A 1 HETATM 20 C C5 SXZ . . . B 2 -34.474 28.45 -4.518 1 26.19 ? C5 SXZ 301 A 1 HETATM 21 C C6 SXZ . . . B 2 -35.659 28.838 -3.904 1 26.69 ? C6 SXZ 301 A 1 HETATM 22 N N6 SXZ . . . B 2 -36.836 28.26 -4.231 1 26.65 ? N6 SXZ 301 A 1 HETATM 23 N N1 SXZ . . . B 2 -35.634 29.816 -2.964 1 26.87 ? N1 SXZ 301 A 1 HETATM 24 C C2 SXZ . . . B 2 -34.483 30.409 -2.612 1 26.69 ? C2 SXZ 301 A 1 HETATM 25 N N3 SXZ . . . B 2 -33.329 30.053 -3.193 1 25.99 ? N3 SXZ 301 A 1 HETATM 26 C C4 SXZ . . . B 2 -33.3 29.08 -4.139 1 26.34 ? C4 SXZ 301 A 1 HETATM 27 C C1 SXZ . . . B 2 -30.837 26.39 -13.058 1 24.18 ? C1 SXZ 301 A 1 HETATM 28 O O2 SXZ . . . B 2 -30.873 25.175 -12.892 1 23.15 ? O2 SXZ 301 A 1 HETATM 29 C C3 SXZ . . . B 2 -30.503 26.986 -14.415 1 23.05 ? C3 SXZ 301 A 1 HETATM 30 C C7 SXZ . . . B 2 -30.612 26.012 -15.589 1 23.08 ? C7 SXZ 301 A 1 HETATM 31 C C9 SXZ . . . B 2 -30.027 26.635 -16.853 1 23.19 ? C9 SXZ 301 A 1 HETATM 32 C C10 SXZ . . . B 2 -32.056 25.595 -15.854 1 22.18 ? C10 SXZ 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #