data_7KW1 # _model_server_result.job_id LYMUtlIgJTsTUYD90TbzqQ _model_server_result.datetime_utc '2024-10-19 03:47:14' _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 7kw1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2500}' # _entry.id 7KW1 # _exptl.entry_id 7KW1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 649.531 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R,5R,7R,8R,10R,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-16-hydroxy-14-[(pyrimidin-4-yl)oxy]-2,10-disulfanyldecahydro-2H,10H-5,8-methano-2lambda~5~,10lambda~5~-cyclopenta[l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione _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 96.57 _cell.angle_gamma 90 _cell.entry_id 7KW1 _cell.length_a 89.221 _cell.length_b 78.653 _cell.length_c 36.026 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KW1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 85.099013 0 35.78941 # _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 'C20 H25 N7 O10 P2 S2' _chem_comp.formula_weight 649.531 _chem_comp.id X4M _chem_comp.mon_nstd_flag . _chem_comp.name (2R,5R,7R,8R,10R,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-16-hydroxy-14-[(pyrimidin-4-yl)oxy]-2,10-disulfanyldecahydro-2H,10H-5,8-methano-2lambda~5~,10lambda~5~-cyclopenta[l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione _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 S29 P40 X4M sing 376 n n P40 O37 X4M doub 377 n n P40 O31 X4M sing 378 n n P40 O35 X4M sing 379 n n C10 C18 X4M sing 380 n n C10 C14 X4M sing 381 n n O31 C12 X4M sing 382 n n C12 C14 X4M sing 383 n n O39 C18 X4M sing 384 n n O39 C6 X4M sing 385 n n O35 C17 X4M sing 386 n n C18 C11 X4M sing 387 n n C1 C6 X4M sing 388 n y C1 C2 X4M doub 389 n y C14 C15 X4M sing 390 n n C6 N22 X4M doub 391 n y N27 C9 X4M sing 392 n n C2 N21 X4M sing 393 n y N22 C3 X4M sing 394 n y C9 N24 X4M doub 395 n n C9 N26 X4M sing 396 n n N21 C3 X4M doub 397 n y O36 C19 X4M sing 398 n n N24 C7 X4M sing 399 n n C17 C19 X4M sing 400 n n C17 C20 X4M sing 401 n n N26 C8 X4M sing 402 n n C15 C11 X4M sing 403 n n C15 O34 X4M sing 404 n n C19 C16 X4M sing 405 n n C7 C5 X4M doub 406 n y C7 N25 X4M sing 407 n y C8 O28 X4M doub 408 n n C8 C5 X4M sing 409 n n C20 N25 X4M sing 410 n n C20 O33 X4M sing 411 n n C5 N23 X4M sing 412 n y N25 C4 X4M sing 413 n y O34 P41 X4M sing 414 n n N23 C4 X4M doub 415 n y C16 O33 X4M sing 416 n n C16 C13 X4M sing 417 n n O32 P41 X4M sing 418 n n O32 C13 X4M sing 419 n n P41 O38 X4M doub 420 n n P41 S30 X4M sing 421 n n C4 H1 X4M sing 422 n n C10 H2 X4M sing 423 n n C10 H3 X4M sing 424 n n C13 H4 X4M sing 425 n n C13 H5 X4M sing 426 n n C15 H6 X4M sing 427 n n C17 H7 X4M sing 428 n n C20 H8 X4M sing 429 n n C1 H9 X4M sing 430 n n C2 H10 X4M sing 431 n n C3 H11 X4M sing 432 n n C11 H12 X4M sing 433 n n C11 H13 X4M sing 434 n n C12 H14 X4M sing 435 n n C12 H15 X4M sing 436 n n C14 H16 X4M sing 437 n n C16 H17 X4M sing 438 n n C18 H18 X4M sing 439 n n C19 H19 X4M sing 440 n n N26 H20 X4M sing 441 n n N27 H21 X4M sing 442 n n N27 H22 X4M sing 443 n n S29 H23 X4M sing 444 n n S30 H24 X4M sing 445 n n O36 H25 X4M sing 446 n n # _atom_sites.entry_id 7KW1 _atom_sites.fract_transf_matrix[1][1] 0.011208 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001291 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012714 _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] 0.027941 _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 X4M A 1 2500 2500 X4M LIG . C 3 HOH A 1 2601 2600 HOH HOH . C 3 HOH A 2 2602 2632 HOH HOH . C 3 HOH A 3 2603 2505 HOH HOH . C 3 HOH A 4 2604 2619 HOH HOH . C 3 HOH A 5 2605 2593 HOH HOH . C 3 HOH A 6 2606 2550 HOH HOH . C 3 HOH A 7 2607 2628 HOH HOH . C 3 HOH A 8 2608 2634 HOH HOH . C 3 HOH A 9 2609 2583 HOH HOH . C 3 HOH A 10 2610 2502 HOH HOH . C 3 HOH A 11 2611 2542 HOH HOH . C 3 HOH A 12 2612 2595 HOH HOH . C 3 HOH A 13 2613 2586 HOH HOH . C 3 HOH A 14 2614 2557 HOH HOH . C 3 HOH A 15 2615 2509 HOH HOH . C 3 HOH A 16 2616 2635 HOH HOH . C 3 HOH A 17 2617 2581 HOH HOH . C 3 HOH A 18 2618 2539 HOH HOH . C 3 HOH A 19 2619 2598 HOH HOH . C 3 HOH A 20 2620 2510 HOH HOH . C 3 HOH A 21 2621 2560 HOH HOH . C 3 HOH A 22 2622 2605 HOH HOH . C 3 HOH A 23 2623 2584 HOH HOH . C 3 HOH A 24 2624 2538 HOH HOH . C 3 HOH A 25 2625 2594 HOH HOH . C 3 HOH A 26 2626 2599 HOH HOH . C 3 HOH A 27 2627 2522 HOH HOH . C 3 HOH A 28 2628 2574 HOH HOH . C 3 HOH A 29 2629 2582 HOH HOH . C 3 HOH A 30 2630 2597 HOH HOH . C 3 HOH A 31 2631 2535 HOH HOH . C 3 HOH A 32 2632 2616 HOH HOH . C 3 HOH A 33 2633 2534 HOH HOH . C 3 HOH A 34 2634 2610 HOH HOH . C 3 HOH A 35 2635 2641 HOH HOH . C 3 HOH A 36 2636 2515 HOH HOH . C 3 HOH A 37 2637 2585 HOH HOH . C 3 HOH A 38 2638 2638 HOH HOH . C 3 HOH A 39 2639 2607 HOH HOH . C 3 HOH A 40 2640 2627 HOH HOH . C 3 HOH A 41 2641 2637 HOH HOH . C 3 HOH A 42 2642 2526 HOH HOH . C 3 HOH A 43 2643 2603 HOH HOH . C 3 HOH A 44 2644 2504 HOH HOH . C 3 HOH A 45 2645 2577 HOH HOH . C 3 HOH A 46 2646 2521 HOH HOH . C 3 HOH A 47 2647 2639 HOH HOH . C 3 HOH A 48 2648 2513 HOH HOH . C 3 HOH A 49 2649 2520 HOH HOH . C 3 HOH A 50 2650 2624 HOH HOH . C 3 HOH A 51 2651 2579 HOH HOH . C 3 HOH A 52 2652 2508 HOH HOH . C 3 HOH A 53 2653 2592 HOH HOH . C 3 HOH A 54 2654 2613 HOH HOH . C 3 HOH A 55 2655 2631 HOH HOH . C 3 HOH A 56 2656 2617 HOH HOH . C 3 HOH A 57 2657 2589 HOH HOH . C 3 HOH A 58 2658 2606 HOH HOH . C 3 HOH A 59 2659 2545 HOH HOH . C 3 HOH A 60 2660 2501 HOH HOH . C 3 HOH A 61 2661 2503 HOH HOH . C 3 HOH A 62 2662 2620 HOH HOH . C 3 HOH A 63 2663 2572 HOH HOH . C 3 HOH A 64 2664 2614 HOH HOH . C 3 HOH A 65 2665 2506 HOH HOH . C 3 HOH A 66 2666 2612 HOH HOH . C 3 HOH A 67 2667 2541 HOH HOH . C 3 HOH A 68 2668 2536 HOH HOH . C 3 HOH A 69 2669 2530 HOH HOH . C 3 HOH A 70 2670 2518 HOH HOH . C 3 HOH A 71 2671 2528 HOH HOH . C 3 HOH A 72 2672 2588 HOH HOH . C 3 HOH A 73 2673 2523 HOH HOH . C 3 HOH A 74 2674 2507 HOH HOH . C 3 HOH A 75 2675 2570 HOH HOH . C 3 HOH A 76 2676 2531 HOH HOH . C 3 HOH A 77 2677 2587 HOH HOH . C 3 HOH A 78 2678 2567 HOH HOH . C 3 HOH A 79 2679 2532 HOH HOH . C 3 HOH A 80 2680 2511 HOH HOH . C 3 HOH A 81 2681 2553 HOH HOH . C 3 HOH A 82 2682 2601 HOH HOH . C 3 HOH A 83 2683 2602 HOH HOH . C 3 HOH A 84 2684 2514 HOH HOH . C 3 HOH A 85 2685 2622 HOH HOH . C 3 HOH A 86 2686 2512 HOH HOH . C 3 HOH A 87 2687 2551 HOH HOH . C 3 HOH A 88 2688 2558 HOH HOH . C 3 HOH A 89 2689 2630 HOH HOH . C 3 HOH A 90 2690 2611 HOH HOH . C 3 HOH A 91 2691 2529 HOH HOH . C 3 HOH A 92 2692 2580 HOH HOH . C 3 HOH A 93 2693 2596 HOH HOH . C 3 HOH A 94 2694 2549 HOH HOH . C 3 HOH A 95 2695 2559 HOH HOH . C 3 HOH A 96 2696 2568 HOH HOH . C 3 HOH A 97 2697 2565 HOH HOH . C 3 HOH A 98 2698 2524 HOH HOH . C 3 HOH A 99 2699 2517 HOH HOH . C 3 HOH A 100 2700 2604 HOH HOH . C 3 HOH A 101 2701 2590 HOH HOH . C 3 HOH A 102 2702 2618 HOH HOH . C 3 HOH A 103 2703 2527 HOH HOH . C 3 HOH A 104 2704 2640 HOH HOH . C 3 HOH A 105 2705 2621 HOH HOH . C 3 HOH A 106 2706 2547 HOH HOH . C 3 HOH A 107 2707 2546 HOH HOH . C 3 HOH A 108 2708 2609 HOH HOH . C 3 HOH A 109 2709 2519 HOH HOH . C 3 HOH A 110 2710 2642 HOH HOH . C 3 HOH A 111 2711 2516 HOH HOH . C 3 HOH A 112 2712 2537 HOH HOH . C 3 HOH A 113 2713 2578 HOH HOH . C 3 HOH A 114 2714 2623 HOH HOH . C 3 HOH A 115 2715 2626 HOH HOH . C 3 HOH A 116 2716 2636 HOH HOH . C 3 HOH A 117 2717 2533 HOH HOH . C 3 HOH A 118 2718 2608 HOH HOH . C 3 HOH A 119 2719 2591 HOH HOH . C 3 HOH A 120 2720 2629 HOH HOH . C 3 HOH A 121 2721 2543 HOH HOH . C 3 HOH A 122 2722 2564 HOH HOH . C 3 HOH A 123 2723 2576 HOH HOH . C 3 HOH A 124 2724 2552 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 C4 X4M . . . B 2 40.837 7.895 19.412 0.5 23.7 ? C4 X4M 2500 A 1 HETATM 2 C C5 X4M . . . B 2 39.551 9.458 18.796 0.5 24.23 ? C5 X4M 2500 A 1 HETATM 3 C C6 X4M . . . B 2 45.929 9.401 16.912 0.5 23.79 ? C6 X4M 2500 A 1 HETATM 4 C C7 X4M . . . B 2 38.899 8.297 18.443 0.5 25.21 ? C7 X4M 2500 A 1 HETATM 5 C C8 X4M . . . B 2 38.919 10.712 18.509 0.5 26.33 ? C8 X4M 2500 A 1 HETATM 6 C C10 X4M . . . B 2 45.556 5.908 15.744 0.5 23.85 ? C10 X4M 2500 A 1 HETATM 7 C C13 X4M . . . B 2 41.698 4.222 20.784 0.5 22.5 ? C13 X4M 2500 A 1 HETATM 8 C C15 X4M . . . B 2 44.703 5.845 17.918 0.5 22.81 ? C15 X4M 2500 A 1 HETATM 9 C C17 X4M . . . B 2 40.704 5.297 17.875 0.5 22.14 ? C17 X4M 2500 A 1 HETATM 10 C C20 X4M . . . B 2 39.586 5.86 18.704 0.5 22.4 ? C20 X4M 2500 A 1 HETATM 11 C C1 X4M . . . B 2 45.185 10.533 16.69 0.5 24.22 ? C1 X4M 2500 A 1 HETATM 12 C C2 X4M . . . B 2 45.675 11.736 17.153 0.5 24.97 ? C2 X4M 2500 A 1 HETATM 13 C C3 X4M . . . B 2 47.545 10.651 17.993 0.5 24.78 ? C3 X4M 2500 A 1 HETATM 14 C C9 X4M . . . B 2 37.113 9.306 17.567 0.5 25.8 ? C9 X4M 2500 A 1 HETATM 15 C C11 X4M . . . B 2 46.083 6.435 17.995 0.5 22.67 ? C11 X4M 2500 A 1 HETATM 16 C C12 X4M . . . B 2 43.411 4.656 16.179 0.5 24.14 ? C12 X4M 2500 A 1 HETATM 17 C C14 X4M . . . B 2 44.789 5.003 16.691 0.5 23.93 ? C14 X4M 2500 A 1 HETATM 18 C C16 X4M . . . B 2 40.499 4.044 19.866 0.5 21.32 ? C16 X4M 2500 A 1 HETATM 19 C C18 X4M . . . B 2 46.238 6.976 16.596 0.5 23.89 ? C18 X4M 2500 A 1 HETATM 20 C C19 X4M . . . B 2 40.869 3.909 18.419 0.5 22.31 ? C19 X4M 2500 A 1 HETATM 21 N N21 X4M . . . B 2 46.849 11.772 17.792 0.5 25.78 ? N21 X4M 2500 A 1 HETATM 22 N N22 X4M . . . B 2 47.096 9.471 17.556 0.5 25.28 ? N22 X4M 2500 A 1 HETATM 23 N N23 X4M . . . B 2 40.754 9.206 19.403 0.5 24.47 ? N23 X4M 2500 A 1 HETATM 24 N N24 X4M . . . B 2 37.695 8.179 17.828 0.5 24.21 ? N24 X4M 2500 A 1 HETATM 25 N N25 X4M . . . B 2 39.75 7.294 18.841 0.5 24.98 ? N25 X4M 2500 A 1 HETATM 26 N N26 X4M . . . B 2 37.703 10.509 17.894 0.5 24.79 ? N26 X4M 2500 A 1 HETATM 27 N N27 X4M . . . B 2 35.885 9.431 16.954 0.5 25.28 ? N27 X4M 2500 A 1 HETATM 28 O O28 X4M . . . B 2 39.407 11.804 18.789 0.5 25.55 ? O28 X4M 2500 A 1 HETATM 29 S S29 X4M . . . B 2 40.922 5.22 13.647 0.5 24.33 ? S29 X4M 2500 A 1 HETATM 30 S S30 X4M . . . B 2 44.895 4.119 21.763 0.5 25.33 ? S30 X4M 2500 A 1 HETATM 31 O O31 X4M . . . B 2 42.778 5.893 15.896 0.5 25.33 ? O31 X4M 2500 A 1 HETATM 32 O O32 X4M . . . B 2 42.476 5.322 20.375 0.5 24.01 ? O32 X4M 2500 A 1 HETATM 33 O O33 X4M . . . B 2 39.668 5.202 19.968 0.5 23.69 ? O33 X4M 2500 A 1 HETATM 34 O O34 X4M . . . B 2 44.547 4.945 19.002 0.5 23.63 ? O34 X4M 2500 A 1 HETATM 35 O O35 X4M . . . B 2 40.331 5.217 16.502 0.5 22.48 ? O35 X4M 2500 A 1 HETATM 36 O O36 X4M . . . B 2 39.86 3.102 17.81 0.5 23.08 ? O36 X4M 2500 A 1 HETATM 37 O O37 X4M . . . B 2 40.871 7.581 15.552 0.5 24.66 ? O37 X4M 2500 A 1 HETATM 38 O O38 X4M . . . B 2 44.375 6.958 20.618 0.5 23.62 ? O38 X4M 2500 A 1 HETATM 39 O O39 X4M . . . B 2 45.472 8.181 16.453 0.5 23.95 ? O39 X4M 2500 A 1 HETATM 40 P P40 X4M . . . B 2 41.219 6.007 15.404 0.5 22.76 ? P40 X4M 2500 A 1 HETATM 41 P P41 X4M . . . B 2 44.106 5.37 20.499 0.5 24.3 ? P41 X4M 2500 A 1 # _model_server_stats.io_time_ms 102 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 41 #