data_7KVZ # _model_server_result.job_id h8Z_2iD2KM09MUUo0Z_gbQ _model_server_result.datetime_utc '2024-11-25 16:56:55' _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 7kvz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2500}' # _entry.id 7KVZ # _exptl.entry_id 7KVZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 617.4 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R,5R,7R,8R,10S,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2,10,16-trihydroxy-14-[(pyrimidin-4-yl)oxy]decahydro-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 96.79 _cell.angle_gamma 90 _cell.entry_id 7KVZ _cell.length_a 89.441 _cell.length_b 78.273 _cell.length_c 35.934 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KVZ _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 85.192499 0 35.681965 # _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 O12 P2' _chem_comp.formula_weight 617.4 _chem_comp.id X5D _chem_comp.mon_nstd_flag . _chem_comp.name (2R,5R,7R,8R,10S,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2,10,16-trihydroxy-14-[(pyrimidin-4-yl)oxy]decahydro-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 O29 P40 X5D doub 376 n n O37 P40 X5D sing 377 n n P40 O31 X5D sing 378 n n P40 O35 X5D sing 379 n n C10 C18 X5D sing 380 n n C10 C14 X5D sing 381 n n O31 C12 X5D sing 382 n n C12 C14 X5D sing 383 n n O35 C17 X5D sing 384 n n O39 C18 X5D sing 385 n n O39 C6 X5D sing 386 n n C1 C6 X5D sing 387 n y C1 C2 X5D doub 388 n y C18 C11 X5D sing 389 n n C14 C15 X5D sing 390 n n N27 C9 X5D sing 391 n n C6 N22 X5D doub 392 n y C2 N21 X5D sing 393 n y C9 N24 X5D doub 394 n n C9 N26 X5D sing 395 n n N22 C3 X5D sing 396 n y N24 C7 X5D sing 397 n n N26 C8 X5D sing 398 n n N21 C3 X5D doub 399 n y C17 C19 X5D sing 400 n n C17 C20 X5D sing 401 n n O36 C19 X5D sing 402 n n C15 C11 X5D sing 403 n n C15 O34 X5D sing 404 n n C7 C5 X5D doub 405 n y C7 N25 X5D sing 406 n y C8 O28 X5D doub 407 n n C8 C5 X5D sing 408 n n C19 C16 X5D sing 409 n n C20 N25 X5D sing 410 n n C20 O33 X5D sing 411 n n C5 N23 X5D sing 412 n y N25 C4 X5D sing 413 n y O34 P41 X5D sing 414 n n N23 C4 X5D doub 415 n y C16 O33 X5D sing 416 n n C16 C13 X5D sing 417 n n O32 P41 X5D sing 418 n n O32 C13 X5D sing 419 n n P41 O38 X5D doub 420 n n P41 O30 X5D sing 421 n n C4 H1 X5D sing 422 n n C10 H2 X5D sing 423 n n C10 H3 X5D sing 424 n n C13 H4 X5D sing 425 n n C13 H5 X5D sing 426 n n C15 H6 X5D sing 427 n n C17 H7 X5D sing 428 n n C20 H8 X5D sing 429 n n C1 H9 X5D sing 430 n n C2 H10 X5D sing 431 n n C3 H11 X5D sing 432 n n C11 H12 X5D sing 433 n n C11 H13 X5D sing 434 n n C12 H14 X5D sing 435 n n C12 H15 X5D sing 436 n n C14 H16 X5D sing 437 n n C16 H17 X5D sing 438 n n C18 H18 X5D sing 439 n n C19 H19 X5D sing 440 n n N26 H20 X5D sing 441 n n N27 H21 X5D sing 442 n n N27 H22 X5D sing 443 n n O30 H23 X5D sing 444 n n O36 H24 X5D sing 445 n n O37 H25 X5D sing 446 n n # _atom_sites.entry_id 7KVZ _atom_sites.fract_transf_matrix[1][1] 0.011181 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001331 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012776 _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] 0.028025 _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 X5D A 1 2500 2500 X5D LIG . C 3 HOH A 1 2601 2502 HOH HOH . C 3 HOH A 2 2602 2551 HOH HOH . C 3 HOH A 3 2603 2531 HOH HOH . C 3 HOH A 4 2604 2545 HOH HOH . C 3 HOH A 5 2605 2533 HOH HOH . C 3 HOH A 6 2606 2534 HOH HOH . C 3 HOH A 7 2607 2508 HOH HOH . C 3 HOH A 8 2608 2553 HOH HOH . C 3 HOH A 9 2609 2506 HOH HOH . C 3 HOH A 10 2610 2546 HOH HOH . C 3 HOH A 11 2611 2558 HOH HOH . C 3 HOH A 12 2612 2525 HOH HOH . C 3 HOH A 13 2613 2511 HOH HOH . C 3 HOH A 14 2614 2552 HOH HOH . C 3 HOH A 15 2615 2540 HOH HOH . C 3 HOH A 16 2616 2519 HOH HOH . C 3 HOH A 17 2617 2518 HOH HOH . C 3 HOH A 18 2618 2504 HOH HOH . C 3 HOH A 19 2619 2550 HOH HOH . C 3 HOH A 20 2620 2522 HOH HOH . C 3 HOH A 21 2621 2509 HOH HOH . C 3 HOH A 22 2622 2542 HOH HOH . C 3 HOH A 23 2623 2527 HOH HOH . C 3 HOH A 24 2624 2556 HOH HOH . C 3 HOH A 25 2625 2514 HOH HOH . C 3 HOH A 26 2626 2530 HOH HOH . C 3 HOH A 27 2627 2520 HOH HOH . C 3 HOH A 28 2628 2544 HOH HOH . C 3 HOH A 29 2629 2547 HOH HOH . C 3 HOH A 30 2630 2521 HOH HOH . C 3 HOH A 31 2631 2528 HOH HOH . C 3 HOH A 32 2632 2559 HOH HOH . C 3 HOH A 33 2633 2543 HOH HOH . C 3 HOH A 34 2634 2524 HOH HOH . C 3 HOH A 35 2635 2541 HOH HOH . C 3 HOH A 36 2636 2513 HOH HOH . C 3 HOH A 37 2637 2505 HOH HOH . C 3 HOH A 38 2638 2549 HOH HOH . C 3 HOH A 39 2639 2557 HOH HOH . C 3 HOH A 40 2640 2535 HOH HOH . C 3 HOH A 41 2641 2510 HOH HOH . C 3 HOH A 42 2642 2538 HOH HOH . C 3 HOH A 43 2643 2517 HOH HOH . C 3 HOH A 44 2644 2501 HOH HOH . C 3 HOH A 45 2645 2515 HOH HOH . C 3 HOH A 46 2646 2537 HOH HOH . C 3 HOH A 47 2647 2503 HOH HOH . C 3 HOH A 48 2648 2554 HOH HOH . C 3 HOH A 49 2649 2516 HOH HOH . C 3 HOH A 50 2650 2536 HOH HOH . C 3 HOH A 51 2651 2523 HOH HOH . C 3 HOH A 52 2652 2507 HOH HOH . C 3 HOH A 53 2653 2529 HOH HOH . C 3 HOH A 54 2654 2555 HOH HOH . C 3 HOH A 55 2655 2548 HOH HOH . C 3 HOH A 56 2656 2512 HOH HOH . C 3 HOH A 57 2657 2526 HOH HOH . C 3 HOH A 58 2658 2532 HOH HOH . C 3 HOH A 59 2659 2539 HOH HOH . C 3 HOH A 60 2660 2560 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 X5D . . . B 2 41.027 7.908 19.421 0.5 31.92 ? C4 X5D 2500 A 1 HETATM 2 C C5 X5D . . . B 2 39.747 9.447 18.737 0.5 32.51 ? C5 X5D 2500 A 1 HETATM 3 C C6 X5D . . . B 2 46.02 9.234 17.006 0.5 34 ? C6 X5D 2500 A 1 HETATM 4 C C7 X5D . . . B 2 39.117 8.282 18.388 0.5 33.37 ? C7 X5D 2500 A 1 HETATM 5 C C8 X5D . . . B 2 39.124 10.69 18.406 0.5 34.56 ? C8 X5D 2500 A 1 HETATM 6 C C10 X5D . . . B 2 45.868 5.762 15.84 0.5 32.06 ? C10 X5D 2500 A 1 HETATM 7 C C13 X5D . . . B 2 41.862 4.068 20.722 0.5 29.64 ? C13 X5D 2500 A 1 HETATM 8 C C15 X5D . . . B 2 44.96 5.648 18.041 0.5 31.86 ? C15 X5D 2500 A 1 HETATM 9 C C17 X5D . . . B 2 40.78 5.172 17.875 0.5 30.73 ? C17 X5D 2500 A 1 HETATM 10 C C20 X5D . . . B 2 39.754 5.869 18.724 0.5 31.14 ? C20 X5D 2500 A 1 HETATM 11 C C1 X5D . . . B 2 45.293 10.352 16.693 0.5 35.49 ? C1 X5D 2500 A 1 HETATM 12 C C2 X5D . . . B 2 45.854 11.532 17.129 0.5 36.55 ? C2 X5D 2500 A 1 HETATM 13 C C3 X5D . . . B 2 47.613 10.445 18.043 0.5 35.63 ? C3 X5D 2500 A 1 HETATM 14 C C9 X5D . . . B 2 37.366 9.242 17.445 0.5 33.58 ? C9 X5D 2500 A 1 HETATM 15 C C11 X5D . . . B 2 46.302 6.328 18.091 0.5 32.27 ? C11 X5D 2500 A 1 HETATM 16 C C12 X5D . . . B 2 43.67 4.575 16.159 0.5 31.75 ? C12 X5D 2500 A 1 HETATM 17 C C14 X5D . . . B 2 45.019 4.893 16.746 0.5 31.42 ? C14 X5D 2500 A 1 HETATM 18 C C16 X5D . . . B 2 40.578 4.04 19.922 0.5 30.58 ? C16 X5D 2500 A 1 HETATM 19 C C18 X5D . . . B 2 46.408 6.878 16.705 0.5 33.1 ? C18 X5D 2500 A 1 HETATM 20 C C19 X5D . . . B 2 40.78 3.78 18.462 0.5 30.8 ? C19 X5D 2500 A 1 HETATM 21 N N21 X5D . . . B 2 47.009 11.609 17.804 0.5 36.21 ? N21 X5D 2500 A 1 HETATM 22 N N22 X5D . . . B 2 47.176 9.24 17.674 0.5 35.6 ? N22 X5D 2500 A 1 HETATM 23 N N23 X5D . . . B 2 40.93 9.214 19.377 0.5 33 ? N23 X5D 2500 A 1 HETATM 24 N N24 X5D . . . B 2 37.937 8.119 17.747 0.5 33.21 ? N24 X5D 2500 A 1 HETATM 25 N N25 X5D . . . B 2 39.955 7.298 18.836 0.5 33.24 ? N25 X5D 2500 A 1 HETATM 26 N N26 X5D . . . B 2 37.931 10.454 17.759 0.5 33.84 ? N26 X5D 2500 A 1 HETATM 27 N N27 X5D . . . B 2 36.17 9.345 16.794 0.5 34.13 ? N27 X5D 2500 A 1 HETATM 28 O O28 X5D . . . B 2 39.607 11.787 18.678 0.5 35.07 ? O28 X5D 2500 A 1 HETATM 29 O O29 X5D . . . B 2 41.478 4.901 14.113 0.5 33.38 ? O29 X5D 2500 A 1 HETATM 30 O O30 X5D . . . B 2 44.794 4.142 21.589 0.5 31.79 ? O30 X5D 2500 A 1 HETATM 31 O O31 X5D . . . B 2 42.912 5.78 16.084 0.5 32.48 ? O31 X5D 2500 A 1 HETATM 32 O O32 X5D . . . B 2 42.643 5.23 20.513 0.5 30.25 ? O32 X5D 2500 A 1 HETATM 33 O O33 X5D . . . B 2 39.858 5.271 20.006 0.5 31.98 ? O33 X5D 2500 A 1 HETATM 34 O O34 X5D . . . B 2 44.834 4.721 19.1 0.5 31.67 ? O34 X5D 2500 A 1 HETATM 35 O O35 X5D . . . B 2 40.426 5.145 16.499 0.5 31.33 ? O35 X5D 2500 A 1 HETATM 36 O O36 X5D . . . B 2 39.651 3.058 17.965 0.5 31.93 ? O36 X5D 2500 A 1 HETATM 37 O O37 X5D . . . B 2 40.952 7.251 15.201 0.5 30.43 ? O37 X5D 2500 A 1 HETATM 38 O O38 X5D . . . B 2 44.726 6.7 20.723 0.5 30.59 ? O38 X5D 2500 A 1 HETATM 39 O O39 X5D . . . B 2 45.541 8.016 16.603 0.5 34.11 ? O39 X5D 2500 A 1 HETATM 40 P P40 X5D . . . B 2 41.447 5.724 15.38 0.5 30.3 ? P40 X5D 2500 A 1 HETATM 41 P P41 X5D . . . B 2 44.277 5.142 20.566 0.5 31.89 ? P41 X5D 2500 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 41 #