data_1UBG # _model_server_result.job_id l1E8koIA1GbNMntD0pvLAA _model_server_result.datetime_utc '2024-12-27 02:55:46' _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 1ubg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":350}' # _entry.id 1UBG # _exptl.entry_id 1UBG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE 5'-TRIPHOSPHATE" _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 1UBG _cell.length_a 102.96 _cell.length_b 102.96 _cell.length_c 73.578 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1UBG _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _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 'C10 H16 N5 O12 P3' _chem_comp.formula_weight 491.182 _chem_comp.id DTP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE 5'-TRIPHOSPHATE" _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 PG O1G DTP doub 70 n n PG O2G DTP sing 71 n n PG O3G DTP sing 72 n n PG O3B DTP sing 73 n n O2G HOG2 DTP sing 74 n n O3G HOG3 DTP sing 75 n n PB O1B DTP doub 76 n n PB O2B DTP sing 77 n n PB O3B DTP sing 78 n n PB O3A DTP sing 79 n n O2B HOB2 DTP sing 80 n n PA O1A DTP doub 81 n n PA O2A DTP sing 82 n n PA O3A DTP sing 83 n n PA O5' DTP sing 84 n n O2A HOA2 DTP sing 85 n n O5' C5' DTP sing 86 n n C5' C4' DTP sing 87 n n C5' "H5'1" DTP sing 88 n n C5' "H5'2" DTP sing 89 n n C4' O4' DTP sing 90 n n C4' C3' DTP sing 91 n n C4' H4' DTP sing 92 n n O4' C1' DTP sing 93 n n C3' O3' DTP sing 94 n n C3' C2' DTP sing 95 n n C3' H3' DTP sing 96 n n O3' HO3' DTP sing 97 n n C2' C1' DTP sing 98 n n C2' "H2'1" DTP sing 99 n n C2' "H2'2" DTP sing 100 n n C1' N9 DTP sing 101 n n C1' H1' DTP sing 102 n n N9 C8 DTP sing 103 n y N9 C4 DTP sing 104 n y C8 N7 DTP doub 105 n y C8 H8 DTP sing 106 n n N7 C5 DTP sing 107 n y C5 C6 DTP sing 108 n y C5 C4 DTP doub 109 n y C6 N6 DTP sing 110 n n C6 N1 DTP doub 111 n y N6 HN61 DTP sing 112 n n N6 HN62 DTP sing 113 n n N1 C2 DTP sing 114 n y C2 N3 DTP doub 115 n y C2 H2 DTP sing 116 n n N3 C4 DTP sing 117 n y # _atom_sites.entry_id 1UBG _atom_sites.fract_transf_matrix[1][1] 0.009713 _atom_sites.fract_transf_matrix[1][2] 0.005608 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011215 _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] 0.013591 _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 DTP A 1 350 331 DTP DTP . C 3 HOH A 1 351 337 HOH WAT . C 3 HOH A 2 352 339 HOH WAT . C 3 HOH A 3 353 344 HOH WAT . C 3 HOH A 4 354 349 HOH WAT . C 3 HOH A 5 355 351 HOH WAT . C 3 HOH A 6 356 353 HOH WAT . C 3 HOH A 7 357 354 HOH WAT . C 3 HOH A 8 358 356 HOH WAT . C 3 HOH A 9 359 358 HOH WAT . C 3 HOH A 10 360 361 HOH WAT . C 3 HOH A 11 361 363 HOH WAT . C 3 HOH A 12 362 365 HOH WAT . C 3 HOH A 13 363 372 HOH WAT . C 3 HOH A 14 364 373 HOH WAT . C 3 HOH A 15 365 386 HOH WAT . C 3 HOH A 16 366 390 HOH WAT . C 3 HOH A 17 367 391 HOH WAT . C 3 HOH A 18 368 392 HOH WAT . C 3 HOH A 19 369 393 HOH WAT . C 3 HOH A 20 370 394 HOH WAT . C 3 HOH A 21 371 396 HOH WAT . C 3 HOH A 22 372 397 HOH WAT . C 3 HOH A 23 373 398 HOH WAT . C 3 HOH A 24 374 404 HOH WAT . C 3 HOH A 25 375 405 HOH WAT . C 3 HOH A 26 376 407 HOH WAT . C 3 HOH A 27 377 415 HOH WAT . C 3 HOH A 28 378 417 HOH WAT . C 3 HOH A 29 379 418 HOH WAT . C 3 HOH A 30 380 419 HOH WAT . C 3 HOH A 31 381 420 HOH WAT . C 3 HOH A 32 382 421 HOH WAT . C 3 HOH A 33 383 426 HOH WAT . C 3 HOH A 34 384 427 HOH WAT . C 3 HOH A 35 385 428 HOH WAT . C 3 HOH A 36 386 430 HOH WAT . C 3 HOH A 37 387 432 HOH WAT . C 3 HOH A 38 388 433 HOH WAT . C 3 HOH A 39 389 434 HOH WAT . C 3 HOH A 40 390 435 HOH WAT . C 3 HOH A 41 391 436 HOH WAT . C 3 HOH A 42 392 439 HOH WAT . C 3 HOH A 43 393 440 HOH WAT . C 3 HOH A 44 394 444 HOH WAT . C 3 HOH A 45 395 451 HOH WAT . C 3 HOH A 46 396 453 HOH WAT . C 3 HOH A 47 397 454 HOH WAT . C 3 HOH A 48 398 455 HOH WAT . C 3 HOH A 49 399 458 HOH WAT . C 3 HOH A 50 400 459 HOH WAT . C 3 HOH A 51 401 460 HOH WAT . C 3 HOH A 52 402 462 HOH WAT . C 3 HOH A 53 403 463 HOH WAT . C 3 HOH A 54 404 464 HOH WAT . C 3 HOH A 55 405 465 HOH WAT . C 3 HOH A 56 406 466 HOH WAT . C 3 HOH A 57 407 467 HOH WAT . C 3 HOH A 58 408 469 HOH WAT . C 3 HOH A 59 409 473 HOH WAT . C 3 HOH A 60 410 474 HOH WAT . C 3 HOH A 61 411 478 HOH WAT . C 3 HOH A 62 412 481 HOH WAT . C 3 HOH A 63 413 483 HOH WAT . C 3 HOH A 64 414 487 HOH WAT . C 3 HOH A 65 415 496 HOH WAT . C 3 HOH A 66 416 497 HOH WAT . C 3 HOH A 67 417 498 HOH WAT . # 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 P PG DTP . . . B 2 5.665 23.294 -6.771 1 75.65 ? PG DTP 350 A 1 HETATM 2 O O1G DTP . . . B 2 7.111 23.472 -6.494 1 75.65 ? O1G DTP 350 A 1 HETATM 3 O O2G DTP . . . B 2 5.119 22.738 -5.615 1 75.65 ? O2G DTP 350 A 1 HETATM 4 O O3G DTP . . . B 2 5.442 22.396 -8.019 1 75.65 ? O3G DTP 350 A 1 HETATM 5 P PB DTP . . . B 2 5.267 26.222 -6.862 1 75.65 ? PB DTP 350 A 1 HETATM 6 O O1B DTP . . . B 2 6.754 26.304 -6.642 1 75.65 ? O1B DTP 350 A 1 HETATM 7 O O2B DTP . . . B 2 4.433 26.867 -5.972 1 75.65 ? O2B DTP 350 A 1 HETATM 8 O O3B DTP . . . B 2 4.808 24.718 -6.935 1 75.65 ? O3B DTP 350 A 1 HETATM 9 P PA DTP . . . B 2 6.074 27.392 -9.352 1 75.65 ? PA DTP 350 A 1 HETATM 10 O O1A DTP . . . B 2 6.58 28.539 -8.589 1 75.65 ? O1A DTP 350 A 1 HETATM 11 O O2A DTP . . . B 2 7.069 26.479 -9.846 1 75.65 ? O2A DTP 350 A 1 HETATM 12 O O3A DTP . . . B 2 4.977 26.831 -8.32 1 75.65 ? O3A DTP 350 A 1 HETATM 13 O O5' DTP . . . B 2 5.294 27.896 -10.498 1 75.65 ? O5' DTP 350 A 1 HETATM 14 C C5' DTP . . . B 2 4.65 27.058 -11.484 1 75.65 ? C5' DTP 350 A 1 HETATM 15 C C4' DTP . . . B 2 4.541 27.715 -12.866 1 75.65 ? C4' DTP 350 A 1 HETATM 16 O O4' DTP . . . B 2 5.6 28.681 -13.035 1 75.65 ? O4' DTP 350 A 1 HETATM 17 C C3' DTP . . . B 2 4.649 26.768 -14.044 1 75.65 ? C3' DTP 350 A 1 HETATM 18 O O3' DTP . . . B 2 3.461 26.822 -14.8 1 75.65 ? O3' DTP 350 A 1 HETATM 19 C C2' DTP . . . B 2 5.86 27.194 -14.848 1 75.65 ? C2' DTP 350 A 1 HETATM 20 C C1' DTP . . . B 2 6.4 28.419 -14.152 1 75.65 ? C1' DTP 350 A 1 HETATM 21 N N9 DTP . . . B 2 7.771 28.256 -13.667 1 75.65 ? N9 DTP 350 A 1 HETATM 22 C C8 DTP . . . B 2 8.39 27.76 -12.566 1 75.65 ? C8 DTP 350 A 1 HETATM 23 N N7 DTP . . . B 2 9.697 27.837 -12.601 1 75.65 ? N7 DTP 350 A 1 HETATM 24 C C5 DTP . . . B 2 9.955 28.414 -13.814 1 75.65 ? C5 DTP 350 A 1 HETATM 25 C C6 DTP . . . B 2 11.18 28.787 -14.497 1 75.65 ? C6 DTP 350 A 1 HETATM 26 N N6 DTP . . . B 2 12.391 28.599 -13.987 1 75.65 ? N6 DTP 350 A 1 HETATM 27 N N1 DTP . . . B 2 11.09 29.372 -15.745 1 75.65 ? N1 DTP 350 A 1 HETATM 28 C C2 DTP . . . B 2 9.866 29.568 -16.284 1 75.65 ? C2 DTP 350 A 1 HETATM 29 N N3 DTP . . . B 2 8.665 29.264 -15.73 1 75.65 ? N3 DTP 350 A 1 HETATM 30 C C4 DTP . . . B 2 8.783 28.684 -14.493 1 75.65 ? C4 DTP 350 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 30 #