data_4WKN # _model_server_result.job_id 2KLDQ5s271gOHQKMq_J33w _model_server_result.datetime_utc '2024-11-29 00:16:38' _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 4wkn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4WKN # _exptl.entry_id 4WKN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 293.388 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(METHYLSULFANYL)METHYL]PYRROLIDIN-3-OL _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 4WKN _cell.length_a 156.958 _cell.length_b 156.958 _cell.length_c 156.958 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WKN _symmetry.cell_setting ? _symmetry.Int_Tables_number 211 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 3 2' # _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' 19_555 -x,-z,-y -1 0 0 0 0 -1 0 -1 0 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 'C13 H19 N5 O S' _chem_comp.formula_weight 293.388 _chem_comp.id TDI _chem_comp.mon_nstd_flag . _chem_comp.name (3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(METHYLSULFANYL)METHYL]PYRROLIDIN-3-OL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms (3R,4S)-1-[9-DEAZAADENIN-9-YL)METHYL]-3-HYDROXY-4-(METHYLTHIOMETHYL)PYRROLIDINE # 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 C2 N1 TDI doub 290 n y C2 N3 TDI sing 291 n y C2 H2 TDI sing 292 n n C4 C5 TDI sing 293 n y C4 C9 TDI sing 294 n y C4 N3 TDI doub 295 n y C5 C6 TDI doub 296 n y C5 N7 TDI sing 297 n y C6 N6 TDI sing 298 n n C6 N1 TDI sing 299 n y CS5 S TDI sing 300 n n CS5 HS51 TDI sing 301 n n CS5 HS52 TDI sing 302 n n CS5 HS53 TDI sing 303 n n S C5' TDI sing 304 n n C5' C4' TDI sing 305 n n C5' "H5'1" TDI sing 306 n n C5' "H5'2" TDI sing 307 n n C4' C1' TDI sing 308 n n C4' C3' TDI sing 309 n n C4' H4' TDI sing 310 n n C1' N1' TDI sing 311 n n C1' "H1'1" TDI sing 312 n n C1' "H1'2" TDI sing 313 n n N1' C10 TDI sing 314 n n N1' C2' TDI sing 315 n n C10 C9 TDI sing 316 n n C10 H101 TDI sing 317 n n C10 H102 TDI sing 318 n n C9 C8 TDI doub 319 n y C8 N7 TDI sing 320 n y C8 H8 TDI sing 321 n n N7 HN7 TDI sing 322 n n N6 HN61 TDI sing 323 n n N6 HN62 TDI sing 324 n n C2' C3' TDI sing 325 n n C2' "H2'1" TDI sing 326 n n C2' "H2'2" TDI sing 327 n n C3' O3' TDI sing 328 n n C3' H3' TDI sing 329 n n O3' H1 TDI sing 330 n n # _atom_sites.entry_id 4WKN _atom_sites.fract_transf_matrix[1][1] 0.006371 _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] 0.006371 _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] 0.006371 _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 TDI A 1 301 1 TDI TDI . C 3 HOH A 1 401 118 HOH HOH . C 3 HOH A 2 402 43 HOH HOH . C 3 HOH A 3 403 119 HOH HOH . C 3 HOH A 4 404 11 HOH HOH . C 3 HOH A 5 405 127 HOH HOH . C 3 HOH A 6 406 20 HOH HOH . C 3 HOH A 7 407 45 HOH HOH . C 3 HOH A 8 408 12 HOH HOH . C 3 HOH A 9 409 111 HOH HOH . C 3 HOH A 10 410 17 HOH HOH . C 3 HOH A 11 411 128 HOH HOH . C 3 HOH A 12 412 28 HOH HOH . C 3 HOH A 13 413 88 HOH HOH . C 3 HOH A 14 414 57 HOH HOH . C 3 HOH A 15 415 21 HOH HOH . C 3 HOH A 16 416 136 HOH HOH . C 3 HOH A 17 417 144 HOH HOH . C 3 HOH A 18 418 81 HOH HOH . C 3 HOH A 19 419 134 HOH HOH . C 3 HOH A 20 420 58 HOH HOH . C 3 HOH A 21 421 6 HOH HOH . C 3 HOH A 22 422 47 HOH HOH . C 3 HOH A 23 423 29 HOH HOH . C 3 HOH A 24 424 3 HOH HOH . C 3 HOH A 25 425 10 HOH HOH . C 3 HOH A 26 426 113 HOH HOH . C 3 HOH A 27 427 7 HOH HOH . C 3 HOH A 28 428 5 HOH HOH . C 3 HOH A 29 429 9 HOH HOH . C 3 HOH A 30 430 87 HOH HOH . C 3 HOH A 31 431 16 HOH HOH . C 3 HOH A 32 432 79 HOH HOH . C 3 HOH A 33 433 8 HOH HOH . C 3 HOH A 34 434 60 HOH HOH . C 3 HOH A 35 435 19 HOH HOH . C 3 HOH A 36 436 138 HOH HOH . C 3 HOH A 37 437 59 HOH HOH . C 3 HOH A 38 438 139 HOH HOH . C 3 HOH A 39 439 22 HOH HOH . C 3 HOH A 40 440 18 HOH HOH . C 3 HOH A 41 441 56 HOH HOH . C 3 HOH A 42 442 77 HOH HOH . C 3 HOH A 43 443 96 HOH HOH . C 3 HOH A 44 444 46 HOH HOH . C 3 HOH A 45 445 31 HOH HOH . C 3 HOH A 46 446 135 HOH HOH . C 3 HOH A 47 447 122 HOH HOH . C 3 HOH A 48 448 25 HOH HOH . C 3 HOH A 49 449 141 HOH HOH . C 3 HOH A 50 450 143 HOH HOH . C 3 HOH A 51 451 140 HOH HOH . C 3 HOH A 52 452 80 HOH HOH . C 3 HOH A 53 453 142 HOH HOH . C 3 HOH A 54 454 133 HOH HOH . C 3 HOH A 55 455 148 HOH HOH . C 3 HOH A 56 456 75 HOH HOH . C 3 HOH A 57 457 94 HOH HOH . C 3 HOH A 58 458 84 HOH HOH . C 3 HOH A 59 459 93 HOH HOH . C 3 HOH A 60 460 26 HOH HOH . C 3 HOH A 61 461 1 HOH HOH . C 3 HOH A 62 462 2 HOH HOH . C 3 HOH A 63 463 4 HOH HOH . C 3 HOH A 64 464 13 HOH HOH . C 3 HOH A 65 465 14 HOH HOH . C 3 HOH A 66 466 15 HOH HOH . C 3 HOH A 67 467 23 HOH HOH . C 3 HOH A 68 468 24 HOH HOH . C 3 HOH A 69 469 27 HOH HOH . C 3 HOH A 70 470 30 HOH HOH . C 3 HOH A 71 471 32 HOH HOH . C 3 HOH A 72 472 33 HOH HOH . C 3 HOH A 73 473 34 HOH HOH . C 3 HOH A 74 474 35 HOH HOH . C 3 HOH A 75 475 36 HOH HOH . C 3 HOH A 76 476 37 HOH HOH . C 3 HOH A 77 477 38 HOH HOH . C 3 HOH A 78 478 39 HOH HOH . C 3 HOH A 79 479 40 HOH HOH . C 3 HOH A 80 480 41 HOH HOH . C 3 HOH A 81 481 42 HOH HOH . C 3 HOH A 82 482 44 HOH HOH . C 3 HOH A 83 483 48 HOH HOH . C 3 HOH A 84 484 49 HOH HOH . C 3 HOH A 85 485 50 HOH HOH . C 3 HOH A 86 486 51 HOH HOH . C 3 HOH A 87 487 52 HOH HOH . C 3 HOH A 88 488 53 HOH HOH . C 3 HOH A 89 489 54 HOH HOH . C 3 HOH A 90 490 55 HOH HOH . C 3 HOH A 91 491 61 HOH HOH . C 3 HOH A 92 492 62 HOH HOH . C 3 HOH A 93 493 63 HOH HOH . C 3 HOH A 94 494 64 HOH HOH . C 3 HOH A 95 495 65 HOH HOH . C 3 HOH A 96 496 66 HOH HOH . C 3 HOH A 97 497 67 HOH HOH . C 3 HOH A 98 498 68 HOH HOH . C 3 HOH A 99 499 69 HOH HOH . C 3 HOH A 100 500 70 HOH HOH . C 3 HOH A 101 501 71 HOH HOH . C 3 HOH A 102 502 72 HOH HOH . C 3 HOH A 103 503 73 HOH HOH . C 3 HOH A 104 504 74 HOH HOH . C 3 HOH A 105 505 76 HOH HOH . C 3 HOH A 106 506 78 HOH HOH . C 3 HOH A 107 507 82 HOH HOH . C 3 HOH A 108 508 83 HOH HOH . C 3 HOH A 109 509 85 HOH HOH . C 3 HOH A 110 510 86 HOH HOH . C 3 HOH A 111 511 89 HOH HOH . C 3 HOH A 112 512 90 HOH HOH . C 3 HOH A 113 513 91 HOH HOH . C 3 HOH A 114 514 92 HOH HOH . C 3 HOH A 115 515 95 HOH HOH . C 3 HOH A 116 516 97 HOH HOH . C 3 HOH A 117 517 98 HOH HOH . C 3 HOH A 118 518 99 HOH HOH . C 3 HOH A 119 519 100 HOH HOH . C 3 HOH A 120 520 101 HOH HOH . C 3 HOH A 121 521 102 HOH HOH . C 3 HOH A 122 522 103 HOH HOH . C 3 HOH A 123 523 104 HOH HOH . C 3 HOH A 124 524 105 HOH HOH . C 3 HOH A 125 525 106 HOH HOH . C 3 HOH A 126 526 107 HOH HOH . C 3 HOH A 127 527 108 HOH HOH . C 3 HOH A 128 528 109 HOH HOH . C 3 HOH A 129 529 110 HOH HOH . C 3 HOH A 130 530 112 HOH HOH . C 3 HOH A 131 531 114 HOH HOH . C 3 HOH A 132 532 115 HOH HOH . C 3 HOH A 133 533 116 HOH HOH . C 3 HOH A 134 534 117 HOH HOH . C 3 HOH A 135 535 120 HOH HOH . C 3 HOH A 136 536 121 HOH HOH . C 3 HOH A 137 537 123 HOH HOH . C 3 HOH A 138 538 124 HOH HOH . C 3 HOH A 139 539 125 HOH HOH . C 3 HOH A 140 540 126 HOH HOH . C 3 HOH A 141 541 129 HOH HOH . C 3 HOH A 142 542 130 HOH HOH . C 3 HOH A 143 543 131 HOH HOH . C 3 HOH A 144 544 132 HOH HOH . C 3 HOH A 145 545 137 HOH HOH . C 3 HOH A 146 546 145 HOH HOH . C 3 HOH A 147 547 146 HOH HOH . C 3 HOH A 148 548 147 HOH HOH . C 3 HOH A 149 549 149 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 C2 TDI . . . B 2 8.025 48.79 -37.079 1 19.17 ? C2 TDI 301 A 1 HETATM 2 C C4 TDI . . . B 2 9.577 48.981 -35.35 1 19.02 ? C4 TDI 301 A 1 HETATM 3 C C5 TDI . . . B 2 10.041 50.178 -35.87 1 18.57 ? C5 TDI 301 A 1 HETATM 4 C C6 TDI . . . B 2 9.446 50.665 -37.037 1 19.19 ? C6 TDI 301 A 1 HETATM 5 C CS5 TDI . . . B 2 14.206 44.262 -37.862 1 22.81 ? CS5 TDI 301 A 1 HETATM 6 S S TDI . . . B 2 12.485 44.654 -37.941 1 22.88 ? S TDI 301 A 1 HETATM 7 C C5' TDI . . . B 2 12.183 45.805 -36.649 1 20.65 ? C5' TDI 301 A 1 HETATM 8 C C4' TDI . . . B 2 12.103 45.131 -35.275 1 19.77 ? C4' TDI 301 A 1 HETATM 9 C C1' TDI . . . B 2 12.083 46.199 -34.173 1 19.19 ? C1' TDI 301 A 1 HETATM 10 N N1' TDI . . . B 2 10.72 46.17 -33.591 1 18.69 ? N1' TDI 301 A 1 HETATM 11 C C10 TDI . . . B 2 10.178 47.486 -33.246 1 18.75 ? C10 TDI 301 A 1 HETATM 12 C C9 TDI . . . B 2 10.315 48.652 -34.207 1 18.65 ? C9 TDI 301 A 1 HETATM 13 C C8 TDI . . . B 2 11.211 49.71 -34.052 1 19.08 ? C8 TDI 301 A 1 HETATM 14 N N7 TDI . . . B 2 11.021 50.608 -35.059 1 19.1 ? N7 TDI 301 A 1 HETATM 15 N N6 TDI . . . B 2 9.855 51.841 -37.592 1 19.08 ? N6 TDI 301 A 1 HETATM 16 N N1 TDI . . . B 2 8.443 49.956 -37.618 1 18.49 ? N1 TDI 301 A 1 HETATM 17 N N3 TDI . . . B 2 8.576 48.289 -35.955 1 18.71 ? N3 TDI 301 A 1 HETATM 18 C C2' TDI . . . B 2 9.863 45.443 -34.571 1 18.87 ? C2' TDI 301 A 1 HETATM 19 C C3' TDI . . . B 2 10.808 44.365 -35.077 1 19.1 ? C3' TDI 301 A 1 HETATM 20 O O3' TDI . . . B 2 11 43.357 -34.074 1 18.69 ? O3' TDI 301 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 20 #