data_1TY8 # _model_server_result.job_id vQbt021xwDJRXZbyQfTDNg _model_server_result.datetime_utc '2024-12-27 03:18:09' _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 1ty8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":285}' # _entry.id 1TY8 # _exptl.entry_id 1TY8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 111.75 _cell.angle_gamma 90 _cell.entry_id 1TY8 _cell.length_a 107.948 _cell.length_b 38.054 _cell.length_c 63.137 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1TY8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PQS monomeric 1 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F 1 1,2 A,B,C,D,E,F 2 1 # 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_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 107.948 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 128 A CYS 128 1_555 A SG CYS 136 A CYS 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 A O PRO 78 A PRO 78 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc2 A O PRO 78 A PRO 78 1_555 C NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? metalc ? metalc3 A O GLY 79 A GLY 79 1_555 C NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc4 A OG1 THR 148 A THR 148 1_555 C NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? metalc ? metalc5 E O1A ADP . A ADP 285 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc6 E O2B ADP . A ADP 285 1_555 C NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.836 ? metalc ? metalc7 B NA NA . A NA 301 1_555 F O HOH . A HOH 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 1TY8 _atom_sites.fract_transf_matrix[1][1] 0.009264 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003696 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026278 _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] 0.017053 _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 NA A 1 301 1 NA NA1 . C 2 NA A 1 302 2 NA NA1 . D 3 CL A 1 303 3 CL CL1 . E 4 ADP A 1 285 285 ADP ADP . F 5 HOH A 1 304 1 HOH TIP . F 5 HOH A 2 305 2 HOH TIP . F 5 HOH A 3 306 3 HOH TIP . F 5 HOH A 4 307 4 HOH TIP . F 5 HOH A 5 308 5 HOH TIP . F 5 HOH A 6 309 6 HOH TIP . F 5 HOH A 7 310 7 HOH TIP . F 5 HOH A 8 311 8 HOH TIP . F 5 HOH A 9 312 9 HOH TIP . F 5 HOH A 10 313 10 HOH TIP . F 5 HOH A 11 314 11 HOH TIP . F 5 HOH A 12 315 12 HOH TIP . F 5 HOH A 13 316 13 HOH TIP . F 5 HOH A 14 317 14 HOH TIP . F 5 HOH A 15 318 15 HOH TIP . F 5 HOH A 16 319 16 HOH TIP . F 5 HOH A 17 320 17 HOH TIP . F 5 HOH A 18 321 18 HOH TIP . F 5 HOH A 19 322 19 HOH TIP . F 5 HOH A 20 323 20 HOH TIP . F 5 HOH A 21 324 21 HOH TIP . F 5 HOH A 22 325 22 HOH TIP . F 5 HOH A 23 326 23 HOH TIP . F 5 HOH A 24 327 24 HOH TIP . F 5 HOH A 25 328 25 HOH TIP . F 5 HOH A 26 329 26 HOH TIP . F 5 HOH A 27 330 27 HOH TIP . F 5 HOH A 28 331 28 HOH TIP . F 5 HOH A 29 332 29 HOH TIP . F 5 HOH A 30 333 30 HOH TIP . F 5 HOH A 31 334 31 HOH TIP . F 5 HOH A 32 335 32 HOH TIP . F 5 HOH A 33 336 33 HOH TIP . F 5 HOH A 34 337 34 HOH TIP . F 5 HOH A 35 338 35 HOH TIP . F 5 HOH A 36 339 36 HOH TIP . F 5 HOH A 37 340 37 HOH TIP . F 5 HOH A 38 341 38 HOH TIP . F 5 HOH A 39 342 39 HOH TIP . F 5 HOH A 40 343 40 HOH TIP . F 5 HOH A 41 344 41 HOH TIP . F 5 HOH A 42 345 42 HOH TIP . F 5 HOH A 43 346 43 HOH TIP . F 5 HOH A 44 347 44 HOH TIP . F 5 HOH A 45 348 45 HOH TIP . F 5 HOH A 46 349 46 HOH TIP . F 5 HOH A 47 350 47 HOH TIP . F 5 HOH A 48 351 48 HOH TIP . F 5 HOH A 49 352 49 HOH TIP . F 5 HOH A 50 353 50 HOH TIP . F 5 HOH A 51 354 51 HOH TIP . F 5 HOH A 52 355 52 HOH TIP . F 5 HOH A 53 356 53 HOH TIP . F 5 HOH A 54 357 54 HOH TIP . F 5 HOH A 55 358 55 HOH TIP . F 5 HOH A 56 359 56 HOH TIP . F 5 HOH A 57 360 57 HOH TIP . F 5 HOH A 58 361 58 HOH TIP . F 5 HOH A 59 362 59 HOH TIP . F 5 HOH A 60 363 60 HOH TIP . F 5 HOH A 61 364 61 HOH TIP . F 5 HOH A 62 365 62 HOH TIP . F 5 HOH A 63 366 63 HOH TIP . F 5 HOH A 64 367 64 HOH TIP . F 5 HOH A 65 368 65 HOH TIP . F 5 HOH A 66 369 66 HOH TIP . F 5 HOH A 67 370 67 HOH TIP . F 5 HOH A 68 371 68 HOH TIP . F 5 HOH A 69 372 69 HOH TIP . F 5 HOH A 70 373 70 HOH TIP . F 5 HOH A 71 374 71 HOH TIP . F 5 HOH A 72 375 72 HOH TIP . F 5 HOH A 73 376 73 HOH TIP . F 5 HOH A 74 377 74 HOH TIP . F 5 HOH A 75 378 75 HOH TIP . F 5 HOH A 76 379 76 HOH TIP . F 5 HOH A 77 380 77 HOH TIP . F 5 HOH A 78 381 78 HOH TIP . F 5 HOH A 79 382 79 HOH TIP . F 5 HOH A 80 383 80 HOH TIP . F 5 HOH A 81 384 81 HOH TIP . F 5 HOH A 82 385 82 HOH TIP . F 5 HOH A 83 386 83 HOH TIP . F 5 HOH A 84 387 84 HOH TIP . F 5 HOH A 85 388 85 HOH TIP . F 5 HOH A 86 389 86 HOH TIP . F 5 HOH A 87 390 87 HOH TIP . F 5 HOH A 88 391 88 HOH TIP . F 5 HOH A 89 392 89 HOH TIP . F 5 HOH A 90 393 90 HOH TIP . F 5 HOH A 91 394 91 HOH TIP . F 5 HOH A 92 395 92 HOH TIP . F 5 HOH A 93 396 93 HOH TIP . F 5 HOH A 94 397 94 HOH TIP . F 5 HOH A 95 398 95 HOH TIP . F 5 HOH A 96 399 96 HOH TIP . F 5 HOH A 97 400 97 HOH TIP . F 5 HOH A 98 401 98 HOH TIP . F 5 HOH A 99 402 99 HOH TIP . F 5 HOH A 100 403 100 HOH TIP . F 5 HOH A 101 404 101 HOH TIP . F 5 HOH A 102 405 102 HOH TIP . F 5 HOH A 103 406 103 HOH TIP . F 5 HOH A 104 407 104 HOH TIP . F 5 HOH A 105 408 105 HOH TIP . F 5 HOH A 106 409 106 HOH TIP . F 5 HOH A 107 410 107 HOH TIP . F 5 HOH A 108 411 108 HOH TIP . F 5 HOH A 109 412 109 HOH TIP . F 5 HOH A 110 413 110 HOH TIP . F 5 HOH A 111 414 111 HOH TIP . F 5 HOH A 112 415 112 HOH TIP . F 5 HOH A 113 416 113 HOH TIP . F 5 HOH A 114 417 114 HOH TIP . F 5 HOH A 115 418 115 HOH TIP . F 5 HOH A 116 419 116 HOH TIP . F 5 HOH A 117 420 117 HOH TIP . F 5 HOH A 118 421 118 HOH TIP . F 5 HOH A 119 422 119 HOH TIP . F 5 HOH A 120 423 120 HOH TIP . F 5 HOH A 121 424 121 HOH TIP . F 5 HOH A 122 425 122 HOH TIP . F 5 HOH A 123 426 123 HOH TIP . F 5 HOH A 124 427 124 HOH TIP . F 5 HOH A 125 428 125 HOH TIP . F 5 HOH A 126 429 126 HOH TIP . F 5 HOH A 127 430 127 HOH TIP . F 5 HOH A 128 431 128 HOH TIP . F 5 HOH A 129 432 129 HOH TIP . F 5 HOH A 130 433 130 HOH TIP . F 5 HOH A 131 434 131 HOH TIP . F 5 HOH A 132 435 132 HOH TIP . F 5 HOH A 133 436 133 HOH TIP . F 5 HOH A 134 437 134 HOH TIP . F 5 HOH A 135 438 135 HOH TIP . F 5 HOH A 136 439 136 HOH TIP . F 5 HOH A 137 440 137 HOH TIP . F 5 HOH A 138 441 138 HOH TIP . F 5 HOH A 139 442 139 HOH TIP . F 5 HOH A 140 443 140 HOH TIP . F 5 HOH A 141 444 141 HOH TIP . F 5 HOH A 142 445 142 HOH TIP . F 5 HOH A 143 446 143 HOH TIP . F 5 HOH A 144 447 144 HOH TIP . F 5 HOH A 145 448 145 HOH TIP . F 5 HOH A 146 449 146 HOH TIP . F 5 HOH A 147 450 147 HOH TIP . F 5 HOH A 148 451 148 HOH TIP . F 5 HOH A 149 452 149 HOH TIP . F 5 HOH A 150 453 150 HOH TIP . F 5 HOH A 151 454 151 HOH TIP . F 5 HOH A 152 455 152 HOH TIP . F 5 HOH A 153 456 153 HOH TIP . F 5 HOH A 154 457 154 HOH TIP . F 5 HOH A 155 458 155 HOH TIP . F 5 HOH A 156 459 156 HOH TIP . F 5 HOH A 157 460 157 HOH TIP . F 5 HOH A 158 461 158 HOH TIP . F 5 HOH A 159 462 159 HOH TIP . F 5 HOH A 160 463 160 HOH TIP . F 5 HOH A 161 464 161 HOH TIP . F 5 HOH A 162 465 162 HOH TIP . F 5 HOH A 163 466 163 HOH TIP . F 5 HOH A 164 467 164 HOH TIP . F 5 HOH A 165 468 165 HOH TIP . F 5 HOH A 166 469 166 HOH TIP . # 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 PB ADP . . . E 4 48.348 0.09 13.328 1 12.7 ? PB ADP 285 A 1 HETATM 2 O O1B ADP . . . E 4 49.399 0.737 12.496 1 12.32 ? O1B ADP 285 A 1 HETATM 3 O O2B ADP . . . E 4 47.034 -0.204 12.462 1 11.46 ? O2B ADP 285 A 1 HETATM 4 O O3B ADP . . . E 4 48.842 -1.177 13.926 1 12.81 ? O3B ADP 285 A 1 HETATM 5 P PA ADP . . . E 4 47.033 0.937 15.81 1 15.76 ? PA ADP 285 A 1 HETATM 6 O O1A ADP . . . E 4 46.228 2.148 16.01 1 18.94 ? O1A ADP 285 A 1 HETATM 7 O O2A ADP . . . E 4 46.171 -0.239 15.798 1 15.39 ? O2A ADP 285 A 1 HETATM 8 O O3A ADP . . . E 4 47.862 1.088 14.456 1 13.11 ? O3A ADP 285 A 1 HETATM 9 O O5' ADP . . . E 4 48.032 0.836 17.012 1 19.42 ? O5' ADP 285 A 1 HETATM 10 C C5' ADP . . . E 4 49.436 0.873 16.954 1 15.71 ? C5' ADP 285 A 1 HETATM 11 C C4' ADP . . . E 4 49.964 0.811 18.414 1 16.59 ? C4' ADP 285 A 1 HETATM 12 O O4' ADP . . . E 4 49.35 1.787 19.289 1 15.61 ? O4' ADP 285 A 1 HETATM 13 C C3' ADP . . . E 4 49.864 -0.535 19.163 1 14.53 ? C3' ADP 285 A 1 HETATM 14 O O3' ADP . . . E 4 51.147 -0.98 19.609 1 15.2 ? O3' ADP 285 A 1 HETATM 15 C C2' ADP . . . E 4 48.869 -0.301 20.323 1 14.73 ? C2' ADP 285 A 1 HETATM 16 O O2' ADP . . . E 4 49.13 -1.125 21.471 1 14.82 ? O2' ADP 285 A 1 HETATM 17 C C1' ADP . . . E 4 49.011 1.175 20.552 1 13.62 ? C1' ADP 285 A 1 HETATM 18 N N9 ADP . . . E 4 47.812 1.885 21.15 1 13.42 ? N9 ADP 285 A 1 HETATM 19 C C8 ADP . . . E 4 46.5 1.686 20.84 1 12.95 ? C8 ADP 285 A 1 HETATM 20 N N7 ADP . . . E 4 45.754 2.494 21.575 1 13.44 ? N7 ADP 285 A 1 HETATM 21 C C5 ADP . . . E 4 46.53 3.211 22.349 1 14.34 ? C5 ADP 285 A 1 HETATM 22 C C6 ADP . . . E 4 46.34 4.214 23.322 1 14.74 ? C6 ADP 285 A 1 HETATM 23 N N6 ADP . . . E 4 45.105 4.637 23.629 1 13.51 ? N6 ADP 285 A 1 HETATM 24 N N1 ADP . . . E 4 47.444 4.777 23.972 1 13.25 ? N1 ADP 285 A 1 HETATM 25 C C2 ADP . . . E 4 48.73 4.387 23.702 1 15.18 ? C2 ADP 285 A 1 HETATM 26 N N3 ADP . . . E 4 48.917 3.424 22.769 1 13.58 ? N3 ADP 285 A 1 HETATM 27 C C4 ADP . . . E 4 47.87 2.821 22.083 1 13.58 ? C4 ADP 285 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #