data_4WKO # _model_server_result.job_id '_CGLNpW0jYoFu0Uodm3mFg' _model_server_result.datetime_utc '2024-11-25 10:43:44' _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 4wko # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4WKO # _exptl.entry_id 4WKO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 351.467 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-hydroxybutyl)sulfanyl]methyl}pyrrolidin-3-ol _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 4WKO _cell.length_a 157.256 _cell.length_b 157.256 _cell.length_c 157.256 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WKO _symmetry.cell_setting ? _symmetry.Int_Tables_number 211 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_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 1,2 # 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' 13_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 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 'C16 H25 N5 O2 S' _chem_comp.formula_weight 351.467 _chem_comp.id GMD _chem_comp.mon_nstd_flag . _chem_comp.name (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-hydroxybutyl)sulfanyl]methyl}pyrrolidin-3-ol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms hydroxybutylthio-DADMe-Immucillin-A # 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 C2 N1 GMD doub 129 n y C2 N3 GMD sing 130 n y N1 C6 GMD sing 131 n y N3 C4 GMD doub 132 n y C6 N6 GMD sing 133 n n C6 C5 GMD doub 134 n y C4 C5 GMD sing 135 n y C4 C9 GMD sing 136 n y C2' N1' GMD sing 137 n n C2' C3' GMD sing 138 n n C5 N7 GMD sing 139 n y C10 C9 GMD sing 140 n n C10 N1' GMD sing 141 n n C9 C8 GMD doub 142 n y N1' C1' GMD sing 143 n n C3' O3' GMD sing 144 n n C3' C4' GMD sing 145 n n N7 C8 GMD sing 146 n y C1' C4' GMD sing 147 n n C4' C5' GMD sing 148 n n C5' S5' GMD sing 149 n n S5' CG GMD sing 150 n n CG CB GMD sing 151 n n CB CA GMD sing 152 n n CA C GMD sing 153 n n OXT C GMD sing 154 n n C H1 GMD sing 155 n n C H2 GMD sing 156 n n OXT H3 GMD sing 157 n n CA H4 GMD sing 158 n n CA H5 GMD sing 159 n n CB H6 GMD sing 160 n n CB H7 GMD sing 161 n n CG H8 GMD sing 162 n n CG H9 GMD sing 163 n n C5' H10 GMD sing 164 n n C5' H11 GMD sing 165 n n C4' H12 GMD sing 166 n n C1' H13 GMD sing 167 n n C1' H14 GMD sing 168 n n C3' H15 GMD sing 169 n n O3' H16 GMD sing 170 n n C2' H17 GMD sing 171 n n C2' H18 GMD sing 172 n n C10 H20 GMD sing 173 n n C10 H21 GMD sing 174 n n C8 H22 GMD sing 175 n n N7 H23 GMD sing 176 n n C2 H24 GMD sing 177 n n N6 H25 GMD sing 178 n n N6 H26 GMD sing 179 n n # _atom_sites.entry_id 4WKO _atom_sites.fract_transf_matrix[1][1] 0.006359 _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] 0.006359 _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] 0.006359 _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 GMD A 1 301 1 GMD BoD . C 3 HOH A 1 401 63 HOH HOH . C 3 HOH A 2 402 107 HOH HOH . C 3 HOH A 3 403 143 HOH HOH . C 3 HOH A 4 404 153 HOH HOH . C 3 HOH A 5 405 142 HOH HOH . C 3 HOH A 6 406 183 HOH HOH . C 3 HOH A 7 407 37 HOH HOH . C 3 HOH A 8 408 174 HOH HOH . C 3 HOH A 9 409 53 HOH HOH . C 3 HOH A 10 410 10 HOH HOH . C 3 HOH A 11 411 12 HOH HOH . C 3 HOH A 12 412 43 HOH HOH . C 3 HOH A 13 413 88 HOH HOH . C 3 HOH A 14 414 6 HOH HOH . C 3 HOH A 15 415 138 HOH HOH . C 3 HOH A 16 416 69 HOH HOH . C 3 HOH A 17 417 29 HOH HOH . C 3 HOH A 18 418 84 HOH HOH . C 3 HOH A 19 419 125 HOH HOH . C 3 HOH A 20 420 7 HOH HOH . C 3 HOH A 21 421 49 HOH HOH . C 3 HOH A 22 422 1 HOH HOH . C 3 HOH A 23 423 122 HOH HOH . C 3 HOH A 24 424 62 HOH HOH . C 3 HOH A 25 425 13 HOH HOH . C 3 HOH A 26 426 81 HOH HOH . C 3 HOH A 27 427 35 HOH HOH . C 3 HOH A 28 428 105 HOH HOH . C 3 HOH A 29 429 8 HOH HOH . C 3 HOH A 30 430 67 HOH HOH . C 3 HOH A 31 431 95 HOH HOH . C 3 HOH A 32 432 59 HOH HOH . C 3 HOH A 33 433 3 HOH HOH . C 3 HOH A 34 434 181 HOH HOH . C 3 HOH A 35 435 31 HOH HOH . C 3 HOH A 36 436 39 HOH HOH . C 3 HOH A 37 437 16 HOH HOH . C 3 HOH A 38 438 28 HOH HOH . C 3 HOH A 39 439 154 HOH HOH . C 3 HOH A 40 440 92 HOH HOH . C 3 HOH A 41 441 70 HOH HOH . C 3 HOH A 42 442 96 HOH HOH . C 3 HOH A 43 443 116 HOH HOH . C 3 HOH A 44 444 155 HOH HOH . C 3 HOH A 45 445 151 HOH HOH . C 3 HOH A 46 446 72 HOH HOH . C 3 HOH A 47 447 97 HOH HOH . C 3 HOH A 48 448 27 HOH HOH . C 3 HOH A 49 449 152 HOH HOH . C 3 HOH A 50 450 144 HOH HOH . C 3 HOH A 51 451 170 HOH HOH . C 3 HOH A 52 452 21 HOH HOH . C 3 HOH A 53 453 196 HOH HOH . C 3 HOH A 54 454 195 HOH HOH . C 3 HOH A 55 455 179 HOH HOH . C 3 HOH A 56 456 124 HOH HOH . C 3 HOH A 57 457 150 HOH HOH . C 3 HOH A 58 458 186 HOH HOH . C 3 HOH A 59 459 80 HOH HOH . C 3 HOH A 60 460 136 HOH HOH . C 3 HOH A 61 461 102 HOH HOH . C 3 HOH A 62 462 164 HOH HOH . C 3 HOH A 63 463 148 HOH HOH . C 3 HOH A 64 464 156 HOH HOH . C 3 HOH A 65 465 58 HOH HOH . C 3 HOH A 66 466 177 HOH HOH . C 3 HOH A 67 467 64 HOH HOH . C 3 HOH A 68 468 83 HOH HOH . C 3 HOH A 69 469 157 HOH HOH . C 3 HOH A 70 470 115 HOH HOH . C 3 HOH A 71 471 171 HOH HOH . C 3 HOH A 72 472 206 HOH HOH . C 3 HOH A 73 473 75 HOH HOH . C 3 HOH A 74 474 207 HOH HOH . C 3 HOH A 75 475 213 HOH HOH . C 3 HOH A 76 476 178 HOH HOH . C 3 HOH A 77 477 134 HOH HOH . C 3 HOH A 78 478 2 HOH HOH . C 3 HOH A 79 479 4 HOH HOH . C 3 HOH A 80 480 5 HOH HOH . C 3 HOH A 81 481 9 HOH HOH . C 3 HOH A 82 482 11 HOH HOH . C 3 HOH A 83 483 14 HOH HOH . C 3 HOH A 84 484 15 HOH HOH . C 3 HOH A 85 485 17 HOH HOH . C 3 HOH A 86 486 18 HOH HOH . C 3 HOH A 87 487 19 HOH HOH . C 3 HOH A 88 488 20 HOH HOH . C 3 HOH A 89 489 22 HOH HOH . C 3 HOH A 90 490 23 HOH HOH . C 3 HOH A 91 491 24 HOH HOH . C 3 HOH A 92 492 25 HOH HOH . C 3 HOH A 93 493 26 HOH HOH . C 3 HOH A 94 494 30 HOH HOH . C 3 HOH A 95 495 32 HOH HOH . C 3 HOH A 96 496 33 HOH HOH . C 3 HOH A 97 497 34 HOH HOH . C 3 HOH A 98 498 36 HOH HOH . C 3 HOH A 99 499 38 HOH HOH . C 3 HOH A 100 500 40 HOH HOH . C 3 HOH A 101 501 41 HOH HOH . C 3 HOH A 102 502 42 HOH HOH . C 3 HOH A 103 503 44 HOH HOH . C 3 HOH A 104 504 45 HOH HOH . C 3 HOH A 105 505 46 HOH HOH . C 3 HOH A 106 506 47 HOH HOH . C 3 HOH A 107 507 48 HOH HOH . C 3 HOH A 108 508 50 HOH HOH . C 3 HOH A 109 509 51 HOH HOH . C 3 HOH A 110 510 52 HOH HOH . C 3 HOH A 111 511 54 HOH HOH . C 3 HOH A 112 512 55 HOH HOH . C 3 HOH A 113 513 56 HOH HOH . C 3 HOH A 114 514 57 HOH HOH . C 3 HOH A 115 515 60 HOH HOH . C 3 HOH A 116 516 61 HOH HOH . C 3 HOH A 117 517 65 HOH HOH . C 3 HOH A 118 518 66 HOH HOH . C 3 HOH A 119 519 68 HOH HOH . C 3 HOH A 120 520 71 HOH HOH . C 3 HOH A 121 521 73 HOH HOH . C 3 HOH A 122 522 74 HOH HOH . C 3 HOH A 123 523 76 HOH HOH . C 3 HOH A 124 524 77 HOH HOH . C 3 HOH A 125 525 78 HOH HOH . C 3 HOH A 126 526 79 HOH HOH . C 3 HOH A 127 527 82 HOH HOH . C 3 HOH A 128 528 85 HOH HOH . C 3 HOH A 129 529 86 HOH HOH . C 3 HOH A 130 530 87 HOH HOH . C 3 HOH A 131 531 89 HOH HOH . C 3 HOH A 132 532 90 HOH HOH . C 3 HOH A 133 533 91 HOH HOH . C 3 HOH A 134 534 93 HOH HOH . C 3 HOH A 135 535 94 HOH HOH . C 3 HOH A 136 536 98 HOH HOH . C 3 HOH A 137 537 99 HOH HOH . C 3 HOH A 138 538 100 HOH HOH . C 3 HOH A 139 539 101 HOH HOH . C 3 HOH A 140 540 103 HOH HOH . C 3 HOH A 141 541 104 HOH HOH . C 3 HOH A 142 542 106 HOH HOH . C 3 HOH A 143 543 108 HOH HOH . C 3 HOH A 144 544 109 HOH HOH . C 3 HOH A 145 545 110 HOH HOH . C 3 HOH A 146 546 111 HOH HOH . C 3 HOH A 147 547 112 HOH HOH . C 3 HOH A 148 548 113 HOH HOH . C 3 HOH A 149 549 114 HOH HOH . C 3 HOH A 150 550 117 HOH HOH . C 3 HOH A 151 551 118 HOH HOH . C 3 HOH A 152 552 119 HOH HOH . C 3 HOH A 153 553 120 HOH HOH . C 3 HOH A 154 554 121 HOH HOH . C 3 HOH A 155 555 123 HOH HOH . C 3 HOH A 156 556 126 HOH HOH . C 3 HOH A 157 557 127 HOH HOH . C 3 HOH A 158 558 128 HOH HOH . C 3 HOH A 159 559 129 HOH HOH . C 3 HOH A 160 560 130 HOH HOH . C 3 HOH A 161 561 131 HOH HOH . C 3 HOH A 162 562 132 HOH HOH . C 3 HOH A 163 563 133 HOH HOH . C 3 HOH A 164 564 135 HOH HOH . C 3 HOH A 165 565 137 HOH HOH . C 3 HOH A 166 566 139 HOH HOH . C 3 HOH A 167 567 140 HOH HOH . C 3 HOH A 168 568 141 HOH HOH . C 3 HOH A 169 569 145 HOH HOH . C 3 HOH A 170 570 146 HOH HOH . C 3 HOH A 171 571 147 HOH HOH . C 3 HOH A 172 572 149 HOH HOH . C 3 HOH A 173 573 158 HOH HOH . C 3 HOH A 174 574 159 HOH HOH . C 3 HOH A 175 575 160 HOH HOH . C 3 HOH A 176 576 161 HOH HOH . C 3 HOH A 177 577 162 HOH HOH . C 3 HOH A 178 578 163 HOH HOH . C 3 HOH A 179 579 165 HOH HOH . C 3 HOH A 180 580 166 HOH HOH . C 3 HOH A 181 581 167 HOH HOH . C 3 HOH A 182 582 168 HOH HOH . C 3 HOH A 183 583 169 HOH HOH . C 3 HOH A 184 584 172 HOH HOH . C 3 HOH A 185 585 173 HOH HOH . C 3 HOH A 186 586 175 HOH HOH . C 3 HOH A 187 587 176 HOH HOH . C 3 HOH A 188 588 180 HOH HOH . C 3 HOH A 189 589 182 HOH HOH . C 3 HOH A 190 590 184 HOH HOH . C 3 HOH A 191 591 185 HOH HOH . C 3 HOH A 192 592 187 HOH HOH . C 3 HOH A 193 593 188 HOH HOH . C 3 HOH A 194 594 189 HOH HOH . C 3 HOH A 195 595 190 HOH HOH . C 3 HOH A 196 596 191 HOH HOH . C 3 HOH A 197 597 192 HOH HOH . C 3 HOH A 198 598 193 HOH HOH . C 3 HOH A 199 599 194 HOH HOH . C 3 HOH A 200 600 197 HOH HOH . C 3 HOH A 201 601 198 HOH HOH . C 3 HOH A 202 602 199 HOH HOH . C 3 HOH A 203 603 200 HOH HOH . C 3 HOH A 204 604 201 HOH HOH . C 3 HOH A 205 605 202 HOH HOH . C 3 HOH A 206 606 203 HOH HOH . C 3 HOH A 207 607 204 HOH HOH . C 3 HOH A 208 608 205 HOH HOH . C 3 HOH A 209 609 208 HOH HOH . C 3 HOH A 210 610 209 HOH HOH . C 3 HOH A 211 611 210 HOH HOH . C 3 HOH A 212 612 211 HOH HOH . C 3 HOH A 213 613 212 HOH HOH . C 3 HOH A 214 614 214 HOH HOH . C 3 HOH A 215 615 215 HOH HOH . C 3 HOH A 216 616 216 HOH HOH . C 3 HOH A 217 617 217 HOH HOH . C 3 HOH A 218 618 218 HOH HOH . C 3 HOH A 219 619 219 HOH HOH . C 3 HOH A 220 620 220 HOH HOH . C 3 HOH A 221 621 221 HOH HOH . C 3 HOH A 222 622 222 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 GMD . . . B 2 -39.766 -43.633 17.433 1 24.11 ? C GMD 301 A 1 HETATM 2 O OXT GMD . . . B 2 -39.967 -42.23 17.275 1 25.74 ? OXT GMD 301 A 1 HETATM 3 C CA GMD . . . B 2 -38.579 -44.043 16.582 1 22.7 ? CA GMD 301 A 1 HETATM 4 C CB GMD . . . B 2 -38.841 -43.93 15.077 1 21.16 ? CB GMD 301 A 1 HETATM 5 C CG GMD . . . B 2 -37.719 -44.675 14.36 1 20.25 ? CG GMD 301 A 1 HETATM 6 S S5' GMD . . . B 2 -37.944 -44.853 12.616 1 18.93 ? S5' GMD 301 A 1 HETATM 7 C C5' GMD . . . B 2 -36.625 -45.932 12.177 1 17.21 ? C5' GMD 301 A 1 HETATM 8 C C4' GMD . . . B 2 -35.27 -45.219 12.126 1 16.11 ? C4' GMD 301 A 1 HETATM 9 C C1' GMD . . . B 2 -34.162 -46.256 12.098 1 15.43 ? C1' GMD 301 A 1 HETATM 10 C C3' GMD . . . B 2 -35.077 -44.436 10.845 1 15.45 ? C3' GMD 301 A 1 HETATM 11 O O3' GMD . . . B 2 -34.04 -43.456 10.955 1 14.86 ? O3' GMD 301 A 1 HETATM 12 C C2' GMD . . . B 2 -34.6 -45.491 9.871 1 15.13 ? C2' GMD 301 A 1 HETATM 13 N N1' GMD . . . B 2 -33.615 -46.205 10.718 1 15.3 ? N1' GMD 301 A 1 HETATM 14 C C10 GMD . . . B 2 -33.243 -47.505 10.152 1 14.61 ? C10 GMD 301 A 1 HETATM 15 C C9 GMD . . . B 2 -34.188 -48.671 10.295 1 14.14 ? C9 GMD 301 A 1 HETATM 16 C C8 GMD . . . B 2 -34.058 -49.745 11.186 1 14.11 ? C8 GMD 301 A 1 HETATM 17 N N7 GMD . . . B 2 -35.072 -50.646 11.007 1 13.59 ? N7 GMD 301 A 1 HETATM 18 C C5 GMD . . . B 2 -35.896 -50.244 10.025 1 13.71 ? C5 GMD 301 A 1 HETATM 19 C C4 GMD . . . B 2 -35.392 -48.983 9.507 1 13.65 ? C4 GMD 301 A 1 HETATM 20 N N3 GMD . . . B 2 -36.013 -48.316 8.504 1 13.36 ? N3 GMD 301 A 1 HETATM 21 C C2 GMD . . . B 2 -37.139 -48.845 7.966 1 13.95 ? C2 GMD 301 A 1 HETATM 22 N N1 GMD . . . B 2 -37.693 -50.016 8.394 1 13.85 ? N1 GMD 301 A 1 HETATM 23 C C6 GMD . . . B 2 -37.131 -50.75 9.391 1 13.83 ? C6 GMD 301 A 1 HETATM 24 N N6 GMD . . . B 2 -37.68 -51.924 9.813 1 13.77 ? N6 GMD 301 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #