data_4DY6 # _model_server_result.job_id vjlKS0t5-75P4TjVtZ0TkQ _model_server_result.datetime_utc '2024-11-13 19:15:34' _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 4dy6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4DY6 # _exptl.entry_id 4DY6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 756.407 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN 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 4DY6 _cell.length_a 63.1 _cell.length_b 75.73 _cell.length_c 118.85 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DY6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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 63.1 0 0 3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 63.1 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 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 'C20 H27 N10 O16 P3' _chem_comp.formula_weight 756.407 _chem_comp.id A22 _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-PHOSPHATE BIS(ADENOSINE)-5'-DIPHOSPHATE" # 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 P2D O2D A22 sing 1 n n P2D O13 A22 doub 2 n n P2D O12 A22 sing 3 n n P2D O11 A22 sing 4 n n O11 H1PA A22 sing 5 n n O12 H2PA A22 sing 6 n n P1A O18 A22 sing 7 n n P1A O15 A22 doub 8 n n P1A O5D A22 sing 9 n n P1A O14 A22 sing 10 n n O14 H5PA A22 sing 11 n n O5D C5D A22 sing 12 n n C5D C4D A22 sing 13 n n C5D HD1 A22 sing 14 n n C5D HD2 A22 sing 15 n n C4D O4D A22 sing 16 n n C4D C3D A22 sing 17 n n C4D H4D A22 sing 18 n n O4D C1D A22 sing 19 n n C3D C2D A22 sing 20 n n C3D O3D A22 sing 21 n n C3D H3CA A22 sing 22 n n O3D H3OA A22 sing 23 n n C2D C1D A22 sing 24 n n C2D O2D A22 sing 25 n n C2D H2D A22 sing 26 n n C1D N9A A22 sing 27 n n C1D H1D A22 sing 28 n n N9A C8A A22 sing 29 n y N9A C4A A22 sing 30 n y C8A N7A A22 doub 31 n y C8A H8A A22 sing 32 n n N7A C5A A22 sing 33 n y C5A C6A A22 sing 34 n y C5A C4A A22 doub 35 n y C6A N6A A22 sing 36 n n C6A N1A A22 doub 37 n y N6A H6A1 A22 sing 38 n n N6A H6A2 A22 sing 39 n n N1A C2A A22 sing 40 n y C2A N3A A22 doub 41 n y C2A H2A A22 sing 42 n n N3A C4A A22 sing 43 n y P1B O5E A22 sing 44 n n P1B O18 A22 sing 45 n n P1B O17 A22 doub 46 n n P1B O16 A22 sing 47 n n O16 H1PB A22 sing 48 n n O5E C5E A22 sing 49 n n C5E C4E A22 sing 50 n n C5E HE1 A22 sing 51 n n C5E HE2 A22 sing 52 n n C4E C3E A22 sing 53 n n C4E O4E A22 sing 54 n n C4E H4E A22 sing 55 n n O4E C1E A22 sing 56 n n C3E C2E A22 sing 57 n n C3E O3E A22 sing 58 n n C3E H3CB A22 sing 59 n n O3E H3OB A22 sing 60 n n C2E O2E A22 sing 61 n n C2E C1E A22 sing 62 n n C2E H2CB A22 sing 63 n n O2E H2OB A22 sing 64 n n C1E N9B A22 sing 65 n n C1E H1E A22 sing 66 n n N9B C8B A22 sing 67 n y N9B C4B A22 sing 68 n y C8B N7B A22 doub 69 n y C8B H8B A22 sing 70 n n N7B C5B A22 sing 71 n y C5B C6B A22 doub 72 n y C5B C4B A22 sing 73 n y C6B N6B A22 sing 74 n n C6B N1B A22 sing 75 n y N6B H6B1 A22 sing 76 n n N6B H6B2 A22 sing 77 n n N1B C2B A22 doub 78 n y C2B N3B A22 sing 79 n y C2B H2B A22 sing 80 n n N3B C4B A22 doub 81 n y # _atom_sites.entry_id 4DY6 _atom_sites.fract_transf_matrix[1][1] 0.015848 _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] 0.013205 _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] 0.008414 _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 A22 A 1 301 273 A22 A22 . C 3 CIT A 1 302 274 CIT CIT . D 4 HOH A 1 401 275 HOH HOH . D 4 HOH A 2 402 276 HOH HOH . D 4 HOH A 3 403 277 HOH HOH . D 4 HOH A 4 404 278 HOH HOH . D 4 HOH A 5 405 279 HOH HOH . D 4 HOH A 6 406 280 HOH HOH . D 4 HOH A 7 407 281 HOH HOH . D 4 HOH A 8 408 282 HOH HOH . D 4 HOH A 9 409 283 HOH HOH . D 4 HOH A 10 410 284 HOH HOH . D 4 HOH A 11 411 285 HOH HOH . D 4 HOH A 12 412 286 HOH HOH . D 4 HOH A 13 413 287 HOH HOH . D 4 HOH A 14 414 288 HOH HOH . D 4 HOH A 15 415 289 HOH HOH . D 4 HOH A 16 416 290 HOH HOH . D 4 HOH A 17 417 291 HOH HOH . D 4 HOH A 18 418 292 HOH HOH . D 4 HOH A 19 419 293 HOH HOH . D 4 HOH A 20 420 294 HOH HOH . D 4 HOH A 21 421 296 HOH HOH . D 4 HOH A 22 422 297 HOH HOH . D 4 HOH A 23 423 298 HOH HOH . D 4 HOH A 24 424 299 HOH HOH . D 4 HOH A 25 425 300 HOH HOH . D 4 HOH A 26 426 301 HOH HOH . D 4 HOH A 27 427 302 HOH HOH . D 4 HOH A 28 428 303 HOH HOH . D 4 HOH A 29 429 304 HOH HOH . D 4 HOH A 30 430 305 HOH HOH . D 4 HOH A 31 431 306 HOH HOH . D 4 HOH A 32 432 307 HOH HOH . D 4 HOH A 33 433 309 HOH HOH . D 4 HOH A 34 434 310 HOH HOH . D 4 HOH A 35 435 311 HOH HOH . D 4 HOH A 36 436 312 HOH HOH . D 4 HOH A 37 437 313 HOH HOH . D 4 HOH A 38 438 314 HOH HOH . D 4 HOH A 39 439 315 HOH HOH . D 4 HOH A 40 440 316 HOH HOH . D 4 HOH A 41 441 317 HOH HOH . D 4 HOH A 42 442 318 HOH HOH . D 4 HOH A 43 443 319 HOH HOH . D 4 HOH A 44 444 320 HOH HOH . D 4 HOH A 45 445 321 HOH HOH . D 4 HOH A 46 446 322 HOH HOH . D 4 HOH A 47 447 323 HOH HOH . D 4 HOH A 48 448 324 HOH HOH . D 4 HOH A 49 449 325 HOH HOH . D 4 HOH A 50 450 326 HOH HOH . D 4 HOH A 51 451 327 HOH HOH . D 4 HOH A 52 452 328 HOH HOH . D 4 HOH A 53 453 329 HOH HOH . D 4 HOH A 54 454 330 HOH HOH . D 4 HOH A 55 455 331 HOH HOH . D 4 HOH A 56 456 332 HOH HOH . D 4 HOH A 57 457 333 HOH HOH . D 4 HOH A 58 458 334 HOH HOH . D 4 HOH A 59 459 335 HOH HOH . D 4 HOH A 60 460 336 HOH HOH . D 4 HOH A 61 461 337 HOH HOH . D 4 HOH A 62 462 338 HOH HOH . D 4 HOH A 63 463 339 HOH HOH . D 4 HOH A 64 464 340 HOH HOH . D 4 HOH A 65 465 341 HOH HOH . D 4 HOH A 66 466 342 HOH HOH . D 4 HOH A 67 467 343 HOH HOH . D 4 HOH A 68 468 344 HOH HOH . D 4 HOH A 69 469 345 HOH HOH . D 4 HOH A 70 470 346 HOH HOH . D 4 HOH A 71 471 347 HOH HOH . D 4 HOH A 72 472 348 HOH HOH . D 4 HOH A 73 473 349 HOH HOH . D 4 HOH A 74 474 350 HOH HOH . D 4 HOH A 75 475 351 HOH HOH . D 4 HOH A 76 476 352 HOH HOH . D 4 HOH A 77 477 353 HOH HOH . D 4 HOH A 78 478 354 HOH HOH . D 4 HOH A 79 479 355 HOH HOH . D 4 HOH A 80 480 356 HOH HOH . D 4 HOH A 81 481 357 HOH HOH . D 4 HOH A 82 482 358 HOH HOH . D 4 HOH A 83 483 359 HOH HOH . D 4 HOH A 84 484 360 HOH HOH . D 4 HOH A 85 485 361 HOH HOH . D 4 HOH A 86 486 362 HOH HOH . D 4 HOH A 87 487 363 HOH HOH . D 4 HOH A 88 488 364 HOH HOH . D 4 HOH A 89 489 365 HOH HOH . D 4 HOH A 90 490 366 HOH HOH . D 4 HOH A 91 491 367 HOH HOH . D 4 HOH A 92 492 370 HOH HOH . D 4 HOH A 93 493 371 HOH HOH . D 4 HOH A 94 494 373 HOH HOH . D 4 HOH A 95 495 381 HOH HOH . D 4 HOH A 96 496 382 HOH HOH . D 4 HOH A 97 497 383 HOH HOH . D 4 HOH A 98 498 384 HOH HOH . D 4 HOH A 99 499 385 HOH HOH . D 4 HOH A 100 500 386 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 P2D A22 . . . B 2 17.348 9.949 17.643 0.9 83.9 ? P2D A22 301 A 1 HETATM 2 O O11 A22 . . . B 2 18.065 10.876 18.594 0.9 83.4 ? O11 A22 301 A 1 HETATM 3 O O12 A22 . . . B 2 17.346 8.497 18.054 0.9 84.95 ? O12 A22 301 A 1 HETATM 4 O O13 A22 . . . B 2 15.992 10.472 17.233 0.9 83.19 ? O13 A22 301 A 1 HETATM 5 P P1A A22 . . . B 2 13.96 7.411 13.223 0.6 82.23 ? P1A A22 301 A 1 HETATM 6 O O14 A22 . . . B 2 13.736 6.234 12.307 0.6 82.23 ? O14 A22 301 A 1 HETATM 7 O O15 A22 . . . B 2 13.694 7.268 14.701 0.6 84.87 ? O15 A22 301 A 1 HETATM 8 O O5D A22 . . . B 2 15.487 7.902 13.021 0.9 81.85 ? O5D A22 301 A 1 HETATM 9 C C5D A22 . . . B 2 16.558 6.957 12.898 0.9 80.59 ? C5D A22 301 A 1 HETATM 10 C C4D A22 . . . B 2 17.819 7.355 13.683 0.9 80.51 ? C4D A22 301 A 1 HETATM 11 O O4D A22 . . . B 2 18.552 8.394 13.026 0.9 77.88 ? O4D A22 301 A 1 HETATM 12 C C3D A22 . . . B 2 17.565 7.876 15.092 0.9 81.44 ? C3D A22 301 A 1 HETATM 13 O O3D A22 . . . B 2 18.502 7.256 15.973 0.9 83.02 ? O3D A22 301 A 1 HETATM 14 C C2D A22 . . . B 2 17.824 9.373 15.047 0.9 80.28 ? C2D A22 301 A 1 HETATM 15 O O2D A22 . . . B 2 18.258 9.941 16.298 0.9 82.25 ? O2D A22 301 A 1 HETATM 16 C C1D A22 . . . B 2 18.917 9.387 13.994 0.9 77.44 ? C1D A22 301 A 1 HETATM 17 N N9A A22 . . . B 2 19.141 10.686 13.316 0.9 74.22 ? N9A A22 301 A 1 HETATM 18 C C8A A22 . . . B 2 18.232 11.575 12.889 0.9 72.51 ? C8A A22 301 A 1 HETATM 19 N N7A A22 . . . B 2 18.882 12.612 12.319 0.9 70.93 ? N7A A22 301 A 1 HETATM 20 C C5A A22 . . . B 2 20.207 12.357 12.379 0.9 70.27 ? C5A A22 301 A 1 HETATM 21 C C6A A22 . . . B 2 21.348 13.036 11.958 0.9 67.48 ? C6A A22 301 A 1 HETATM 22 N N6A A22 . . . B 2 21.251 14.236 11.338 0.9 65.43 ? N6A A22 301 A 1 HETATM 23 N N1A A22 . . . B 2 22.559 12.477 12.185 0.9 66.24 ? N1A A22 301 A 1 HETATM 24 C C2A A22 . . . B 2 22.675 11.295 12.808 0.9 67.57 ? C2A A22 301 A 1 HETATM 25 N N3A A22 . . . B 2 21.595 10.622 13.217 0.9 69.46 ? N3A A22 301 A 1 HETATM 26 C C4A A22 . . . B 2 20.357 11.134 13.009 0.9 71.61 ? C4A A22 301 A 1 HETATM 27 P P1B A22 . . . B 2 13.267 10.172 12.918 0.6 79.43 ? P1B A22 301 A 1 HETATM 28 O O16 A22 . . . B 2 14.227 10.333 14.075 0.6 81.09 ? O16 A22 301 A 1 HETATM 29 O O17 A22 . . . B 2 11.901 10.818 12.956 0.6 78.49 ? O17 A22 301 A 1 HETATM 30 O O18 A22 . . . B 2 13.034 8.599 12.643 0.6 80.42 ? O18 A22 301 A 1 HETATM 31 O O5E A22 . . . B 2 13.999 10.722 11.594 0.6 75.81 ? O5E A22 301 A 1 HETATM 32 C C5E A22 . . . B 2 14.049 9.959 10.393 0.9 72.54 ? C5E A22 301 A 1 HETATM 33 C C4E A22 . . . B 2 15.491 9.858 9.918 0.9 70.36 ? C4E A22 301 A 1 HETATM 34 O O4E A22 . . . B 2 16.019 8.532 10.057 0.9 70.63 ? O4E A22 301 A 1 HETATM 35 C C3E A22 . . . B 2 15.603 10.195 8.446 0.9 65.87 ? C3E A22 301 A 1 HETATM 36 O O3E A22 . . . B 2 15.666 11.617 8.28 0.9 63.03 ? O3E A22 301 A 1 HETATM 37 C C2E A22 . . . B 2 16.833 9.413 8.01 0.9 64.78 ? C2E A22 301 A 1 HETATM 38 O O2E A22 . . . B 2 17.98 10.27 7.905 0.9 61.1 ? O2E A22 301 A 1 HETATM 39 C C1E A22 . . . B 2 17.029 8.314 9.076 0.9 67.71 ? C1E A22 301 A 1 HETATM 40 N N9B A22 . . . B 2 16.955 6.962 8.448 0.9 68.29 ? N9B A22 301 A 1 HETATM 41 C C8B A22 . . . B 2 15.88 6.383 7.879 0.9 68.48 ? C8B A22 301 A 1 HETATM 42 N N7B A22 . . . B 2 16.224 5.169 7.389 0.9 67.16 ? N7B A22 301 A 1 HETATM 43 C C5B A22 . . . B 2 17.542 4.985 7.632 0.9 67.79 ? C5B A22 301 A 1 HETATM 44 C C6B A22 . . . B 2 18.459 3.956 7.363 0.9 66.64 ? C6B A22 301 A 1 HETATM 45 N N6B A22 . . . B 2 18.095 2.814 6.722 0.9 65.59 ? N6B A22 301 A 1 HETATM 46 N N1B A22 . . . B 2 19.741 4.109 7.762 0.9 65.46 ? N1B A22 301 A 1 HETATM 47 C C2B A22 . . . B 2 20.127 5.22 8.403 0.9 66.19 ? C2B A22 301 A 1 HETATM 48 N N3B A22 . . . B 2 19.275 6.209 8.673 0.9 67.25 ? N3B A22 301 A 1 HETATM 49 C C4B A22 . . . B 2 17.984 6.124 8.297 0.9 67.98 ? C4B A22 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 225 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 49 #