data_4K47 # _model_server_result.job_id WqdNRPzKdwVyGhF3BQWN0w _model_server_result.datetime_utc '2025-02-05 05:59:43' _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 4k47 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4K47 # _exptl.entry_id 4K47 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 568.26 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "[(1R,5R,6R,8S)-6-(6-aminopurin-9-yl)-3'-[(R)-oxidanyl(phenyl)methyl]spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1,3,5-triene]-8-yl]methyl dihydrogen phosphate" _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 4K47 _cell.length_a 88.354 _cell.length_b 88.354 _cell.length_c 137.163 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4K47 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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,G _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 'C24 H24 B N5 O9 P -1' _chem_comp.formula_weight 568.26 _chem_comp.id WMP _chem_comp.mon_nstd_flag . _chem_comp.name "[(1R,5R,6R,8S)-6-(6-aminopurin-9-yl)-3'-[(R)-oxidanyl(phenyl)methyl]spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1,3,5-triene]-8-yl]methyl dihydrogen phosphate" _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 CAP OAU WMP sing 380 n n CAP CBC WMP sing 381 n n OAU BA WMP sing 382 n n CBC CAL WMP doub 383 n y CBC CBD WMP sing 384 n y CAL CAK WMP sing 385 n y N6 C6 WMP sing 386 n n BA O2' WMP sing 387 n n BA CBD WMP sing 388 n n BA O3' WMP sing 389 n n N7 C5 WMP sing 390 n y N7 C8 WMP doub 391 n y O2' C2' WMP sing 392 n n C6 C5 WMP doub 393 n y C6 N1 WMP sing 394 n y C5 C4 WMP sing 395 n y C8 N9 WMP sing 396 n y N1 C2 WMP doub 397 n y C2' C1' WMP sing 398 n n C2' C3' WMP sing 399 n n CBD CAN WMP doub 400 n y N9 C4 WMP sing 401 n y N9 C1' WMP sing 402 n n C4 N3 WMP doub 403 n y O3' C3' WMP sing 404 n n CAK CBB WMP doub 405 n y C2 N3 WMP sing 406 n y C1' O4' WMP sing 407 n n C3' C4' WMP sing 408 n n CAN CBB WMP sing 409 n y CBB CBG WMP sing 410 n n C4' O4' WMP sing 411 n n C4' C5' WMP sing 412 n n CBG OAB WMP sing 413 n n CBG CBA WMP sing 414 n n C5' O5' WMP sing 415 n n CBA CAJ WMP doub 416 n y CBA CAI WMP sing 417 n y CAJ CAH WMP sing 418 n y O5' PBM WMP sing 419 n n CAI CAG WMP doub 420 n y CAH CAF WMP doub 421 n y OAD PBM WMP doub 422 n n CAG CAF WMP sing 423 n y PBM OAC WMP sing 424 n n PBM OAE WMP sing 425 n n CAI H1 WMP sing 426 n n CAG H2 WMP sing 427 n n CAF H3 WMP sing 428 n n CAH H4 WMP sing 429 n n CAJ H5 WMP sing 430 n n CBG H6 WMP sing 431 n n OAB H7 WMP sing 432 n n CAN H8 WMP sing 433 n n CAK H9 WMP sing 434 n n CAL H10 WMP sing 435 n n CAP H11 WMP sing 436 n n CAP H12 WMP sing 437 n n C2' H13 WMP sing 438 n n C3' H14 WMP sing 439 n n C4' H15 WMP sing 440 n n C5' H16 WMP sing 441 n n C5' H17 WMP sing 442 n n OAE H18 WMP sing 443 n n OAC H19 WMP sing 444 n n C1' H20 WMP sing 445 n n C8 H21 WMP sing 446 n n C2 H22 WMP sing 447 n n N6 H23 WMP sing 448 n n N6 H24 WMP sing 449 n n # _atom_sites.entry_id 4K47 _atom_sites.fract_transf_matrix[1][1] 0.011318 _atom_sites.fract_transf_matrix[1][2] 0.006535 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013069 _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] 0.007291 _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 WMP A 1 501 1 WMP DRG . C 3 SO4 A 1 502 1 SO4 SO4 . D 3 SO4 A 1 503 2 SO4 SO4 . E 3 SO4 A 1 504 3 SO4 SO4 . F 3 SO4 A 1 505 4 SO4 SO4 . G 4 HOH A 1 601 1 HOH HOH . G 4 HOH A 2 602 2 HOH HOH . G 4 HOH A 3 603 3 HOH HOH . G 4 HOH A 4 604 4 HOH HOH . G 4 HOH A 5 605 5 HOH HOH . G 4 HOH A 6 606 6 HOH HOH . G 4 HOH A 7 607 7 HOH HOH . G 4 HOH A 8 608 8 HOH HOH . G 4 HOH A 9 609 9 HOH HOH . G 4 HOH A 10 610 10 HOH HOH . G 4 HOH A 11 611 11 HOH HOH . G 4 HOH A 12 612 12 HOH HOH . G 4 HOH A 13 613 13 HOH HOH . G 4 HOH A 14 614 14 HOH HOH . G 4 HOH A 15 615 15 HOH HOH . G 4 HOH A 16 616 16 HOH HOH . G 4 HOH A 17 617 17 HOH HOH . G 4 HOH A 18 618 18 HOH HOH . G 4 HOH A 19 619 19 HOH HOH . G 4 HOH A 20 620 20 HOH HOH . G 4 HOH A 21 621 21 HOH HOH . G 4 HOH A 22 622 22 HOH HOH . G 4 HOH A 23 623 23 HOH HOH . G 4 HOH A 24 624 24 HOH HOH . G 4 HOH A 25 625 25 HOH HOH . G 4 HOH A 26 626 26 HOH HOH . G 4 HOH A 27 627 27 HOH HOH . G 4 HOH A 28 628 28 HOH HOH . G 4 HOH A 29 629 29 HOH HOH . G 4 HOH A 30 630 30 HOH HOH . G 4 HOH A 31 631 31 HOH HOH . G 4 HOH A 32 632 32 HOH HOH . G 4 HOH A 33 633 33 HOH HOH . G 4 HOH A 34 634 34 HOH HOH . G 4 HOH A 35 635 35 HOH HOH . G 4 HOH A 36 636 36 HOH HOH . G 4 HOH A 37 637 37 HOH HOH . G 4 HOH A 38 638 38 HOH HOH . G 4 HOH A 39 639 39 HOH HOH . G 4 HOH A 40 640 40 HOH HOH . G 4 HOH A 41 641 41 HOH HOH . G 4 HOH A 42 642 42 HOH HOH . G 4 HOH A 43 643 43 HOH HOH . G 4 HOH A 44 644 44 HOH HOH . G 4 HOH A 45 645 45 HOH HOH . G 4 HOH A 46 646 46 HOH HOH . G 4 HOH A 47 647 47 HOH HOH . G 4 HOH A 48 648 48 HOH HOH . G 4 HOH A 49 649 49 HOH HOH . G 4 HOH A 50 650 50 HOH HOH . G 4 HOH A 51 651 51 HOH HOH . G 4 HOH A 52 652 52 HOH HOH . G 4 HOH A 53 653 53 HOH HOH . G 4 HOH A 54 654 54 HOH HOH . G 4 HOH A 55 655 55 HOH HOH . G 4 HOH A 56 656 56 HOH HOH . G 4 HOH A 57 657 57 HOH HOH . G 4 HOH A 58 658 58 HOH HOH . G 4 HOH A 59 659 59 HOH HOH . G 4 HOH A 60 660 60 HOH HOH . G 4 HOH A 61 661 61 HOH HOH . G 4 HOH A 62 662 62 HOH HOH . G 4 HOH A 63 663 63 HOH HOH . G 4 HOH A 64 664 64 HOH HOH . G 4 HOH A 65 665 65 HOH HOH . G 4 HOH A 66 666 66 HOH HOH . G 4 HOH A 67 667 67 HOH HOH . G 4 HOH A 68 668 68 HOH HOH . G 4 HOH A 69 669 69 HOH HOH . G 4 HOH A 70 670 70 HOH HOH . G 4 HOH A 71 671 71 HOH HOH . G 4 HOH A 72 672 72 HOH HOH . G 4 HOH A 73 673 73 HOH HOH . G 4 HOH A 74 674 74 HOH HOH . G 4 HOH A 75 675 75 HOH HOH . G 4 HOH A 76 676 76 HOH HOH . G 4 HOH A 77 677 77 HOH HOH . G 4 HOH A 78 678 78 HOH HOH . G 4 HOH A 79 679 79 HOH HOH . G 4 HOH A 80 680 80 HOH HOH . G 4 HOH A 81 681 81 HOH HOH . G 4 HOH A 82 682 82 HOH HOH . G 4 HOH A 83 683 83 HOH HOH . G 4 HOH A 84 684 84 HOH HOH . G 4 HOH A 85 685 85 HOH HOH . G 4 HOH A 86 686 86 HOH HOH . G 4 HOH A 87 687 87 HOH HOH . G 4 HOH A 88 688 88 HOH HOH . G 4 HOH A 89 689 89 HOH HOH . G 4 HOH A 90 690 90 HOH HOH . G 4 HOH A 91 691 91 HOH HOH . G 4 HOH A 92 692 92 HOH HOH . G 4 HOH A 93 693 93 HOH HOH . G 4 HOH A 94 694 94 HOH HOH . G 4 HOH A 95 695 95 HOH HOH . G 4 HOH A 96 696 96 HOH HOH . G 4 HOH A 97 697 97 HOH HOH . G 4 HOH A 98 698 98 HOH HOH . G 4 HOH A 99 699 99 HOH HOH . G 4 HOH A 100 700 100 HOH HOH . G 4 HOH A 101 701 101 HOH HOH . G 4 HOH A 102 702 102 HOH HOH . G 4 HOH A 103 703 103 HOH HOH . G 4 HOH A 104 704 104 HOH HOH . G 4 HOH A 105 705 105 HOH HOH . G 4 HOH A 106 706 106 HOH HOH . G 4 HOH A 107 707 107 HOH HOH . G 4 HOH A 108 708 108 HOH HOH . G 4 HOH A 109 709 109 HOH HOH . G 4 HOH A 110 710 110 HOH HOH . G 4 HOH A 111 711 111 HOH HOH . G 4 HOH A 112 712 112 HOH HOH . G 4 HOH A 113 713 113 HOH HOH . G 4 HOH A 114 714 114 HOH HOH . G 4 HOH A 115 715 115 HOH HOH . G 4 HOH A 116 716 116 HOH HOH . G 4 HOH A 117 717 117 HOH HOH . G 4 HOH A 118 718 118 HOH HOH . G 4 HOH A 119 719 119 HOH HOH . G 4 HOH A 120 720 120 HOH HOH . G 4 HOH A 121 721 121 HOH HOH . G 4 HOH A 122 722 122 HOH HOH . G 4 HOH A 123 723 123 HOH HOH . G 4 HOH A 124 724 124 HOH HOH . G 4 HOH A 125 725 125 HOH HOH . G 4 HOH A 126 726 126 HOH HOH . G 4 HOH A 127 727 127 HOH HOH . G 4 HOH A 128 728 128 HOH HOH . G 4 HOH A 129 729 129 HOH HOH . G 4 HOH A 130 730 130 HOH HOH . G 4 HOH A 131 731 131 HOH HOH . G 4 HOH A 132 732 132 HOH HOH . G 4 HOH A 133 733 133 HOH HOH . G 4 HOH A 134 734 134 HOH HOH . G 4 HOH A 135 735 135 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 CAI WMP . . . B 2 14.714 -14.413 11.989 1 47.52 ? CAI WMP 501 A 1 HETATM 2 C CAG WMP . . . B 2 13.739 -14.451 12.984 1 47.63 ? CAG WMP 501 A 1 HETATM 3 C CAF WMP . . . B 2 13.151 -15.659 13.337 1 48.24 ? CAF WMP 501 A 1 HETATM 4 C CAH WMP . . . B 2 13.54 -16.824 12.698 1 48.03 ? CAH WMP 501 A 1 HETATM 5 C CAJ WMP . . . B 2 14.511 -16.791 11.707 1 46.99 ? CAJ WMP 501 A 1 HETATM 6 C CBA WMP . . . B 2 15.104 -15.581 11.346 1 45.1 ? CBA WMP 501 A 1 HETATM 7 C CBG WMP . . . B 2 16.172 -15.522 10.278 1 42.05 ? CBG WMP 501 A 1 HETATM 8 O OAB WMP . . . B 2 17.371 -15.925 10.898 1 41.71 ? OAB WMP 501 A 1 HETATM 9 C CBB WMP . . . B 2 15.871 -16.256 8.991 1 39.32 ? CBB WMP 501 A 1 HETATM 10 C CAN WMP . . . B 2 16.122 -17.625 8.82 1 37.7 ? CAN WMP 501 A 1 HETATM 11 C CBD WMP . . . B 2 15.895 -18.243 7.562 1 36.3 ? CBD WMP 501 A 1 HETATM 12 C CAK WMP . . . B 2 15.359 -15.514 7.938 1 37.32 ? CAK WMP 501 A 1 HETATM 13 C CAL WMP . . . B 2 15.083 -16.134 6.732 1 35.88 ? CAL WMP 501 A 1 HETATM 14 C CBC WMP . . . B 2 15.318 -17.5 6.576 1 35.35 ? CBC WMP 501 A 1 HETATM 15 C CAP WMP . . . B 2 15.153 -18.392 5.327 1 34.58 ? CAP WMP 501 A 1 HETATM 16 O OAU WMP . . . B 2 15.312 -19.768 5.765 1 33.9 ? OAU WMP 501 A 1 HETATM 17 B BA WMP . . . B 2 15.992 -19.758 7.039 1 35.26 ? BA WMP 501 A 1 HETATM 18 O O3' WMP . . . B 2 15.424 -20.91 7.828 1 36.85 ? O3' WMP 501 A 1 HETATM 19 O O2' WMP . . . B 2 17.481 -19.938 7.092 1 35.1 ? O2' WMP 501 A 1 HETATM 20 C C2' WMP . . . B 2 17.658 -21.244 7.562 1 35.86 ? C2' WMP 501 A 1 HETATM 21 C C3' WMP . . . B 2 16.547 -21.306 8.558 1 37.59 ? C3' WMP 501 A 1 HETATM 22 C C4' WMP . . . B 2 16.955 -22.305 9.473 1 39.08 ? C4' WMP 501 A 1 HETATM 23 C C5' WMP . . . B 2 16.382 -22.297 10.727 1 41.67 ? C5' WMP 501 A 1 HETATM 24 O O5' WMP . . . B 2 17.242 -22.531 11.778 1 44.96 ? O5' WMP 501 A 1 HETATM 25 P PBM WMP . . . B 2 16.715 -23.087 13.127 1 48.32 ? PBM WMP 501 A 1 HETATM 26 O OAD WMP . . . B 2 16.188 -24.457 12.867 1 46.74 ? OAD WMP 501 A 1 HETATM 27 O OAE WMP . . . B 2 17.922 -23.211 14.076 1 47.65 ? OAE WMP 501 A 1 HETATM 28 O OAC WMP . . . B 2 15.661 -22.175 13.673 1 48.17 ? OAC WMP 501 A 1 HETATM 29 O O4' WMP . . . B 2 18.497 -21.868 9.573 1 34.96 ? O4' WMP 501 A 1 HETATM 30 C C1' WMP . . . B 2 18.855 -21.951 8.196 1 34.05 ? C1' WMP 501 A 1 HETATM 31 N N9 WMP . . . B 2 19.272 -23.308 7.732 1 31.29 ? N9 WMP 501 A 1 HETATM 32 C C8 WMP . . . B 2 18.49 -24.348 7.381 1 30.57 ? C8 WMP 501 A 1 HETATM 33 N N7 WMP . . . B 2 19.26 -25.398 7.088 1 29.53 ? N7 WMP 501 A 1 HETATM 34 C C5 WMP . . . B 2 20.545 -25.075 7.355 1 30.06 ? C5 WMP 501 A 1 HETATM 35 C C4 WMP . . . B 2 20.541 -23.748 7.792 1 28.73 ? C4 WMP 501 A 1 HETATM 36 N N3 WMP . . . B 2 21.707 -23.157 8.1 1 28.93 ? N3 WMP 501 A 1 HETATM 37 C C2 WMP . . . B 2 22.85 -23.839 8.032 1 28.85 ? C2 WMP 501 A 1 HETATM 38 N N1 WMP . . . B 2 22.905 -25.093 7.555 1 31.01 ? N1 WMP 501 A 1 HETATM 39 C C6 WMP . . . B 2 21.775 -25.726 7.217 1 29.45 ? C6 WMP 501 A 1 HETATM 40 N N6 WMP . . . B 2 21.882 -27.103 6.741 1 31.88 ? N6 WMP 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 40 #