data_7KVX # _model_server_result.job_id NW3yy9NdEjAjXp5qjO4Slw _model_server_result.datetime_utc '2024-10-19 03:47:13' _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 7kvx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7KVX # _exptl.entry_id 7KVX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 648.546 _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)amino]-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 96.52 _cell.angle_gamma 90 _cell.entry_id 7KVX _cell.length_a 89.495 _cell.length_b 78.539 _cell.length_c 36.01 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KVX _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 85.406063 0 35.777097 # _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 H26 N8 O9 P2 S2' _chem_comp.formula_weight 648.546 _chem_comp.id X5J _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)amino]-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 S40 P38 X5J sing 376 n n O30 P38 X5J doub 377 n n P38 O32 X5J sing 378 n n P38 O36 X5J sing 379 n n C10 C15 X5J sing 380 n n C10 C14 X5J sing 381 n n O32 C12 X5J sing 382 n n C12 C14 X5J sing 383 n n N28 C15 X5J sing 384 n n N28 C6 X5J sing 385 n n C1 C6 X5J sing 386 n y C1 C2 X5J doub 387 n y C15 C11 X5J sing 388 n n C6 N22 X5J doub 389 n y O36 C18 X5J sing 390 n n C14 C16 X5J sing 391 n n C2 N21 X5J sing 392 n y N27 C9 X5J sing 393 n n N22 C3 X5J sing 394 n y N21 C3 X5J doub 395 n y C9 N26 X5J sing 396 n n C9 N24 X5J doub 397 n n N26 C8 X5J sing 398 n n N24 C7 X5J sing 399 n n C16 C11 X5J sing 400 n n C16 O35 X5J sing 401 n n C18 C19 X5J sing 402 n n C18 C20 X5J sing 403 n n O37 C19 X5J sing 404 n n C8 O29 X5J doub 405 n n C8 C5 X5J sing 406 n n C7 C5 X5J doub 407 n y C7 N25 X5J sing 408 n y C19 C17 X5J sing 409 n n C5 N23 X5J sing 410 n y C20 N25 X5J sing 411 n n C20 O34 X5J sing 412 n n N25 C4 X5J sing 413 n y O35 P39 X5J sing 414 n n N23 C4 X5J doub 415 n y C17 O34 X5J sing 416 n n C17 C13 X5J sing 417 n n P39 O33 X5J sing 418 n n P39 O31 X5J doub 419 n n P39 S41 X5J sing 420 n n O33 C13 X5J sing 421 n n C4 H1 X5J sing 422 n n C10 H2 X5J sing 423 n n C10 H3 X5J sing 424 n n C13 H4 X5J sing 425 n n C13 H5 X5J sing 426 n n C15 H6 X5J sing 427 n n C17 H7 X5J sing 428 n n C20 H8 X5J sing 429 n n C1 H9 X5J sing 430 n n C2 H10 X5J sing 431 n n C3 H11 X5J sing 432 n n C11 H12 X5J sing 433 n n C11 H13 X5J sing 434 n n C12 H14 X5J sing 435 n n C12 H15 X5J sing 436 n n C14 H16 X5J sing 437 n n C16 H17 X5J sing 438 n n C18 H18 X5J sing 439 n n C19 H19 X5J sing 440 n n N26 H20 X5J sing 441 n n N27 H21 X5J sing 442 n n N27 H22 X5J sing 443 n n N28 H23 X5J sing 444 n n O37 H24 X5J sing 445 n n S40 H25 X5J sing 446 n n S41 H26 X5J sing 447 n n # _atom_sites.entry_id 7KVX _atom_sites.fract_transf_matrix[1][1] 0.011174 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001276 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012733 _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] 0.027951 _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 X5J A 1 401 401 X5J LIG . C 3 HOH A 1 501 14 HOH HOH . C 3 HOH A 2 502 29 HOH HOH . C 3 HOH A 3 503 5 HOH HOH . C 3 HOH A 4 504 36 HOH HOH . C 3 HOH A 5 505 39 HOH HOH . C 3 HOH A 6 506 21 HOH HOH . C 3 HOH A 7 507 3 HOH HOH . C 3 HOH A 8 508 10 HOH HOH . C 3 HOH A 9 509 9 HOH HOH . C 3 HOH A 10 510 1 HOH HOH . C 3 HOH A 11 511 35 HOH HOH . C 3 HOH A 12 512 25 HOH HOH . C 3 HOH A 13 513 19 HOH HOH . C 3 HOH A 14 514 33 HOH HOH . C 3 HOH A 15 515 44 HOH HOH . C 3 HOH A 16 516 38 HOH HOH . C 3 HOH A 17 517 18 HOH HOH . C 3 HOH A 18 518 24 HOH HOH . C 3 HOH A 19 519 34 HOH HOH . C 3 HOH A 20 520 13 HOH HOH . C 3 HOH A 21 521 15 HOH HOH . C 3 HOH A 22 522 43 HOH HOH . C 3 HOH A 23 523 45 HOH HOH . C 3 HOH A 24 524 27 HOH HOH . C 3 HOH A 25 525 32 HOH HOH . C 3 HOH A 26 526 46 HOH HOH . C 3 HOH A 27 527 26 HOH HOH . C 3 HOH A 28 528 31 HOH HOH . C 3 HOH A 29 529 16 HOH HOH . C 3 HOH A 30 530 11 HOH HOH . C 3 HOH A 31 531 4 HOH HOH . C 3 HOH A 32 532 6 HOH HOH . C 3 HOH A 33 533 20 HOH HOH . C 3 HOH A 34 534 8 HOH HOH . C 3 HOH A 35 535 22 HOH HOH . C 3 HOH A 36 536 12 HOH HOH . C 3 HOH A 37 537 41 HOH HOH . C 3 HOH A 38 538 23 HOH HOH . C 3 HOH A 39 539 40 HOH HOH . C 3 HOH A 40 540 37 HOH HOH . C 3 HOH A 41 541 2 HOH HOH . C 3 HOH A 42 542 7 HOH HOH . C 3 HOH A 43 543 30 HOH HOH . C 3 HOH A 44 544 42 HOH HOH . C 3 HOH A 45 545 28 HOH HOH . C 3 HOH A 46 546 17 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 X5J . . . B 2 41.104 7.974 19.433 0.5 38.03 ? C4 X5J 401 A 1 HETATM 2 C C5 X5J . . . B 2 39.626 9.322 18.684 0.5 37.1 ? C5 X5J 401 A 1 HETATM 3 C C6 X5J . . . B 2 45.906 9.223 16.679 0.5 41.98 ? C6 X5J 401 A 1 HETATM 4 C C7 X5J . . . B 2 39.115 8.061 18.49 0.5 38.16 ? C7 X5J 401 A 1 HETATM 5 C C8 X5J . . . B 2 38.823 10.453 18.269 0.5 38.66 ? C8 X5J 401 A 1 HETATM 6 C C10 X5J . . . B 2 45.816 5.66 15.777 0.5 38.25 ? C10 X5J 401 A 1 HETATM 7 C C13 X5J . . . B 2 42.136 4.016 20.77 0.5 39.57 ? C13 X5J 401 A 1 HETATM 8 C C15 X5J . . . B 2 46.288 6.879 16.539 0.5 40.83 ? C15 X5J 401 A 1 HETATM 9 C C17 X5J . . . B 2 40.786 3.905 20.113 0.5 39.39 ? C17 X5J 401 A 1 HETATM 10 C C20 X5J . . . B 2 39.929 5.743 18.96 0.5 39 ? C20 X5J 401 A 1 HETATM 11 C C1 X5J . . . B 2 45.155 10.354 16.459 0.5 40.93 ? C1 X5J 401 A 1 HETATM 12 C C2 X5J . . . B 2 45.673 11.561 16.87 0.5 40.6 ? C2 X5J 401 A 1 HETATM 13 C C3 X5J . . . B 2 47.508 10.52 17.635 0.5 44.05 ? C3 X5J 401 A 1 HETATM 14 C C9 X5J . . . B 2 37.194 8.683 17.556 0.5 34.86 ? C9 X5J 401 A 1 HETATM 15 C C11 X5J . . . B 2 46.153 6.445 17.973 0.5 40.21 ? C11 X5J 401 A 1 HETATM 16 C C12 X5J . . . B 2 43.576 4.534 16.162 0.5 37.78 ? C12 X5J 401 A 1 HETATM 17 C C14 X5J . . . B 2 44.922 4.876 16.725 0.5 38.39 ? C14 X5J 401 A 1 HETATM 18 C C16 X5J . . . B 2 44.846 5.707 17.968 0.5 39.53 ? C16 X5J 401 A 1 HETATM 19 C C18 X5J . . . B 2 40.865 4.975 18.059 0.5 39.52 ? C18 X5J 401 A 1 HETATM 20 C C19 X5J . . . B 2 40.889 3.574 18.657 0.5 41.1 ? C19 X5J 401 A 1 HETATM 21 N N21 X5J . . . B 2 46.861 11.681 17.466 0.5 41.87 ? N21 X5J 401 A 1 HETATM 22 N N22 X5J . . . B 2 47.101 9.294 17.273 0.5 44.97 ? N22 X5J 401 A 1 HETATM 23 N N23 X5J . . . B 2 40.861 9.259 19.274 0.5 37.62 ? N23 X5J 401 A 1 HETATM 24 N N24 X5J . . . B 2 37.935 7.7 17.943 0.5 36.31 ? N24 X5J 401 A 1 HETATM 25 N N25 X5J . . . B 2 40.068 7.199 18.967 0.5 39.87 ? N25 X5J 401 A 1 HETATM 26 N N26 X5J . . . B 2 37.608 10.003 17.71 0.5 36.48 ? N26 X5J 401 A 1 HETATM 27 N N27 X5J . . . B 2 35.99 8.442 16.983 0.5 32.21 ? N27 X5J 401 A 1 HETATM 28 N N28 X5J . . . B 2 45.38 7.991 16.255 0.5 43.36 ? N28 X5J 401 A 1 HETATM 29 O O29 X5J . . . B 2 39.2 11.623 18.415 0.5 37.28 ? O29 X5J 401 A 1 HETATM 30 O O30 X5J . . . B 2 40.892 7.151 15.207 0.5 43.82 ? O30 X5J 401 A 1 HETATM 31 O O31 X5J . . . B 2 44.818 6.797 20.973 0.5 43.87 ? O31 X5J 401 A 1 HETATM 32 O O32 X5J . . . B 2 42.855 5.743 16.028 0.5 41.96 ? O32 X5J 401 A 1 HETATM 33 O O33 X5J . . . B 2 42.727 5.291 20.635 0.5 42.08 ? O33 X5J 401 A 1 HETATM 34 O O34 X5J . . . B 2 40.067 5.139 20.23 0.5 39.67 ? O34 X5J 401 A 1 HETATM 35 O O35 X5J . . . B 2 44.788 4.896 19.126 0.5 42.42 ? O35 X5J 401 A 1 HETATM 36 O O36 X5J . . . B 2 40.426 5.047 16.716 0.5 42.62 ? O36 X5J 401 A 1 HETATM 37 O O37 X5J . . . B 2 39.798 2.709 18.264 0.5 41.57 ? O37 X5J 401 A 1 HETATM 38 P P38 X5J . . . B 2 41.309 5.743 15.523 0.5 42.86 ? P38 X5J 401 A 1 HETATM 39 P P39 X5J . . . B 2 44.352 5.408 20.621 0.5 43.04 ? P39 X5J 401 A 1 HETATM 40 S S40 X5J . . . B 2 41.082 4.44 13.906 0.5 47.64 ? S40 X5J 401 A 1 HETATM 41 S S41 X5J . . . B 2 45.165 3.94 21.864 0.5 47.15 ? S41 X5J 401 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 362 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 41 #