data_3PYG # _model_server_result.job_id IgPKUBM41KJoQ6W5aniHHA _model_server_result.datetime_utc '2025-01-02 17:15:13' _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 3pyg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":307}' # _entry.id 3PYG # _exptl.entry_id 3PYG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 90 _cell.angle_gamma 90 _cell.entry_id 3PYG _cell.length_a 51.199 _cell.length_b 73.122 _cell.length_c 106.958 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PYG _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 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 3PYG _atom_sites.fract_transf_matrix[1][1] 0.019532 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013676 _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] 0.009349 _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 ADP A 1 307 1 ADP ADP . C 3 HOH A 1 308 1 HOH HOH . C 3 HOH A 2 309 2 HOH HOH . C 3 HOH A 3 310 3 HOH HOH . C 3 HOH A 4 311 4 HOH HOH . C 3 HOH A 5 312 5 HOH HOH . C 3 HOH A 6 313 6 HOH HOH . C 3 HOH A 7 314 7 HOH HOH . C 3 HOH A 8 315 9 HOH HOH . C 3 HOH A 9 316 10 HOH HOH . C 3 HOH A 10 317 12 HOH HOH . C 3 HOH A 11 318 13 HOH HOH . C 3 HOH A 12 319 14 HOH HOH . C 3 HOH A 13 320 15 HOH HOH . C 3 HOH A 14 321 16 HOH HOH . C 3 HOH A 15 322 17 HOH HOH . C 3 HOH A 16 323 18 HOH HOH . C 3 HOH A 17 324 19 HOH HOH . C 3 HOH A 18 325 20 HOH HOH . C 3 HOH A 19 326 21 HOH HOH . C 3 HOH A 20 327 22 HOH HOH . C 3 HOH A 21 328 23 HOH HOH . C 3 HOH A 22 329 24 HOH HOH . C 3 HOH A 23 330 25 HOH HOH . C 3 HOH A 24 331 26 HOH HOH . C 3 HOH A 25 332 27 HOH HOH . C 3 HOH A 26 333 28 HOH HOH . C 3 HOH A 27 334 29 HOH HOH . C 3 HOH A 28 335 30 HOH HOH . C 3 HOH A 29 336 31 HOH HOH . C 3 HOH A 30 337 32 HOH HOH . C 3 HOH A 31 338 33 HOH HOH . C 3 HOH A 32 339 34 HOH HOH . C 3 HOH A 33 340 35 HOH HOH . C 3 HOH A 34 341 36 HOH HOH . C 3 HOH A 35 342 37 HOH HOH . C 3 HOH A 36 343 38 HOH HOH . C 3 HOH A 37 344 39 HOH HOH . C 3 HOH A 38 345 40 HOH HOH . C 3 HOH A 39 346 41 HOH HOH . C 3 HOH A 40 347 42 HOH HOH . C 3 HOH A 41 348 43 HOH HOH . C 3 HOH A 42 349 44 HOH HOH . C 3 HOH A 43 350 45 HOH HOH . C 3 HOH A 44 351 46 HOH HOH . C 3 HOH A 45 352 47 HOH HOH . C 3 HOH A 46 353 48 HOH HOH . C 3 HOH A 47 354 49 HOH HOH . C 3 HOH A 48 355 50 HOH HOH . C 3 HOH A 49 356 51 HOH HOH . C 3 HOH A 50 357 52 HOH HOH . C 3 HOH A 51 358 53 HOH HOH . C 3 HOH A 52 359 54 HOH HOH . C 3 HOH A 53 360 55 HOH HOH . C 3 HOH A 54 361 56 HOH HOH . C 3 HOH A 55 362 57 HOH HOH . C 3 HOH A 56 363 58 HOH HOH . C 3 HOH A 57 364 59 HOH HOH . C 3 HOH A 58 365 60 HOH HOH . C 3 HOH A 59 366 61 HOH HOH . C 3 HOH A 60 367 62 HOH HOH . C 3 HOH A 61 368 63 HOH HOH . C 3 HOH A 62 369 64 HOH HOH . C 3 HOH A 63 370 65 HOH HOH . C 3 HOH A 64 371 66 HOH HOH . C 3 HOH A 65 372 67 HOH HOH . C 3 HOH A 66 373 68 HOH HOH . C 3 HOH A 67 374 69 HOH HOH . C 3 HOH A 68 375 70 HOH HOH . C 3 HOH A 69 376 71 HOH HOH . C 3 HOH A 70 377 72 HOH HOH . C 3 HOH A 71 378 73 HOH HOH . C 3 HOH A 72 379 74 HOH HOH . C 3 HOH A 73 380 75 HOH HOH . C 3 HOH A 74 381 76 HOH HOH . C 3 HOH A 75 382 77 HOH HOH . C 3 HOH A 76 383 78 HOH HOH . C 3 HOH A 77 384 79 HOH HOH . C 3 HOH A 78 385 80 HOH HOH . C 3 HOH A 79 386 81 HOH HOH . C 3 HOH A 80 387 82 HOH HOH . C 3 HOH A 81 388 83 HOH HOH . C 3 HOH A 82 389 84 HOH HOH . C 3 HOH A 83 390 85 HOH HOH . C 3 HOH A 84 391 87 HOH HOH . C 3 HOH A 85 392 88 HOH HOH . C 3 HOH A 86 393 89 HOH HOH . C 3 HOH A 87 394 90 HOH HOH . C 3 HOH A 88 395 91 HOH HOH . C 3 HOH A 89 396 92 HOH HOH . C 3 HOH A 90 397 93 HOH HOH . C 3 HOH A 91 398 94 HOH HOH . C 3 HOH A 92 399 95 HOH HOH . C 3 HOH A 93 400 96 HOH HOH . C 3 HOH A 94 401 97 HOH HOH . C 3 HOH A 95 402 98 HOH HOH . C 3 HOH A 96 403 99 HOH HOH . C 3 HOH A 97 404 100 HOH HOH . C 3 HOH A 98 405 101 HOH HOH . C 3 HOH A 99 406 102 HOH HOH . C 3 HOH A 100 407 103 HOH HOH . C 3 HOH A 101 408 104 HOH HOH . C 3 HOH A 102 409 105 HOH HOH . C 3 HOH A 103 410 106 HOH HOH . C 3 HOH A 104 411 107 HOH HOH . C 3 HOH A 105 412 108 HOH HOH . C 3 HOH A 106 413 109 HOH HOH . C 3 HOH A 107 414 110 HOH HOH . C 3 HOH A 108 415 111 HOH HOH . C 3 HOH A 109 416 112 HOH HOH . C 3 HOH A 110 417 113 HOH HOH . C 3 HOH A 111 418 114 HOH HOH . C 3 HOH A 112 419 115 HOH HOH . C 3 HOH A 113 420 116 HOH HOH . C 3 HOH A 114 421 117 HOH HOH . C 3 HOH A 115 422 118 HOH HOH . C 3 HOH A 116 423 119 HOH HOH . C 3 HOH A 117 424 120 HOH HOH . C 3 HOH A 118 425 121 HOH HOH . C 3 HOH A 119 426 122 HOH HOH . C 3 HOH A 120 427 123 HOH HOH . C 3 HOH A 121 428 124 HOH HOH . C 3 HOH A 122 429 125 HOH HOH . C 3 HOH A 123 430 126 HOH HOH . C 3 HOH A 124 431 127 HOH HOH . C 3 HOH A 125 432 128 HOH HOH . C 3 HOH A 126 433 129 HOH HOH . C 3 HOH A 127 434 130 HOH HOH . C 3 HOH A 128 435 131 HOH HOH . C 3 HOH A 129 436 133 HOH HOH . C 3 HOH A 130 437 135 HOH HOH . C 3 HOH A 131 438 136 HOH HOH . C 3 HOH A 132 439 137 HOH HOH . C 3 HOH A 133 440 138 HOH HOH . C 3 HOH A 134 441 139 HOH HOH . C 3 HOH A 135 442 140 HOH HOH . C 3 HOH A 136 443 141 HOH HOH . C 3 HOH A 137 444 142 HOH HOH . C 3 HOH A 138 445 143 HOH HOH . C 3 HOH A 139 446 144 HOH HOH . C 3 HOH A 140 447 145 HOH HOH . C 3 HOH A 141 448 146 HOH HOH . C 3 HOH A 142 449 147 HOH HOH . C 3 HOH A 143 450 148 HOH HOH . C 3 HOH A 144 451 149 HOH HOH . C 3 HOH A 145 452 150 HOH HOH . C 3 HOH A 146 453 151 HOH HOH . C 3 HOH A 147 454 152 HOH HOH . C 3 HOH A 148 455 153 HOH HOH . C 3 HOH A 149 456 154 HOH HOH . C 3 HOH A 150 457 155 HOH HOH . C 3 HOH A 151 458 156 HOH HOH . C 3 HOH A 152 459 157 HOH HOH . C 3 HOH A 153 460 158 HOH HOH . C 3 HOH A 154 461 159 HOH HOH . C 3 HOH A 155 462 160 HOH HOH . C 3 HOH A 156 463 161 HOH HOH . C 3 HOH A 157 464 162 HOH HOH . C 3 HOH A 158 465 163 HOH HOH . C 3 HOH A 159 466 164 HOH HOH . C 3 HOH A 160 467 165 HOH HOH . C 3 HOH A 161 468 166 HOH HOH . C 3 HOH A 162 469 167 HOH HOH . C 3 HOH A 163 470 168 HOH HOH . C 3 HOH A 164 471 169 HOH HOH . C 3 HOH A 165 472 170 HOH HOH . C 3 HOH A 166 473 171 HOH HOH . C 3 HOH A 167 474 172 HOH HOH . C 3 HOH A 168 475 173 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 P PB ADP . . . B 2 -10.973 -13.735 8.036 1 65.12 ? PB ADP 307 A 1 HETATM 2 O O1B ADP . . . B 2 -11.818 -14.589 7.095 1 64.26 ? O1B ADP 307 A 1 HETATM 3 O O2B ADP . . . B 2 -11.728 -12.839 8.996 1 66.89 ? O2B ADP 307 A 1 HETATM 4 O O3B ADP . . . B 2 -9.983 -14.59 8.81 1 62.89 ? O3B ADP 307 A 1 HETATM 5 P PA ADP . . . B 2 -9.5 -11.411 7.516 1 58.84 ? PA ADP 307 A 1 HETATM 6 O O1A ADP . . . B 2 -8.545 -12.377 8.122 1 58.03 ? O1A ADP 307 A 1 HETATM 7 O O2A ADP . . . B 2 -9.059 -10.514 6.374 1 50.71 ? O2A ADP 307 A 1 HETATM 8 O O3A ADP . . . B 2 -10.489 -12.565 7.042 1 62.02 ? O3A ADP 307 A 1 HETATM 9 O O5' ADP . . . B 2 -10.218 -10.491 8.637 1 66.26 ? O5' ADP 307 A 1 HETATM 10 C C5' ADP . . . B 2 -10.075 -10.534 10.061 1 77.57 ? C5' ADP 307 A 1 HETATM 11 C C4' ADP . . . B 2 -11.503 -10.421 10.578 1 86.94 ? C4' ADP 307 A 1 HETATM 12 O O4' ADP . . . B 2 -11.679 -10.646 11.983 1 92.71 ? O4' ADP 307 A 1 HETATM 13 C C3' ADP . . . B 2 -12.308 -9.14 10.282 1 91.21 ? C3' ADP 307 A 1 HETATM 14 O O3' ADP . . . B 2 -12.761 -8.998 8.921 1 89.77 ? O3' ADP 307 A 1 HETATM 15 C C2' ADP . . . B 2 -13.528 -9.392 11.146 1 94.74 ? C2' ADP 307 A 1 HETATM 16 O O2' ADP . . . B 2 -14.624 -9.765 10.29 1 96.64 ? O2' ADP 307 A 1 HETATM 17 C C1' ADP . . . B 2 -13.128 -10.607 12 1 96.4 ? C1' ADP 307 A 1 HETATM 18 N N9 ADP . . . B 2 -13.864 -10.741 13.305 1 99.9 ? N9 ADP 307 A 1 HETATM 19 C C8 ADP . . . B 2 -13.337 -10.814 14.556 1 101.19 ? C8 ADP 307 A 1 HETATM 20 N N7 ADP . . . B 2 -14.321 -10.959 15.493 1 102.56 ? N7 ADP 307 A 1 HETATM 21 C C5 ADP . . . B 2 -15.519 -10.997 14.835 1 103 ? C5 ADP 307 A 1 HETATM 22 C C6 ADP . . . B 2 -16.971 -11.133 15.183 1 102.77 ? C6 ADP 307 A 1 HETATM 23 N N6 ADP . . . B 2 -17.356 -11.268 16.474 1 103.11 ? N6 ADP 307 A 1 HETATM 24 N N1 ADP . . . B 2 -17.902 -11.125 14.187 1 102.55 ? N1 ADP 307 A 1 HETATM 25 C C2 ADP . . . B 2 -17.555 -10.995 12.891 1 102.12 ? C2 ADP 307 A 1 HETATM 26 N N3 ADP . . . B 2 -16.266 -10.864 12.501 1 102.09 ? N3 ADP 307 A 1 HETATM 27 C C4 ADP . . . B 2 -15.215 -10.858 13.393 1 102.08 ? C4 ADP 307 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #