data_5DAU # _model_server_result.job_id tVpz5Tvzm7kDMYhNCyZI-g _model_server_result.datetime_utc '2024-11-22 16:35:24' _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 5dau # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 5DAU # _exptl.entry_id 5DAU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-3',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 93.52 _cell.angle_gamma 90 _cell.entry_id 5DAU _cell.length_a 31.178 _cell.length_b 60.353 _cell.length_c 38.425 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DAU _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,D _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 3 _struct_asym.id C _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 metalc ? metalc1 A OD2 ASP 21 A ASP 21 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? metalc ? metalc4 A OE2 GLU 43 A GLU 43 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.882 ? metalc ? metalc5 B CA CA . A CA 201 1_555 C O6P THP . A THP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.17 ? metalc ? metalc6 B CA CA . A CA 201 1_555 D O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? metalc ? metalc7 B CA CA . A CA 201 1_555 D O HOH . A HOH 374 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id THP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-3',5'-DIPHOSPHATE" _chem_comp.type 'dna linking' _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 P2 O4P THP doub 277 n n P2 O5P THP sing 278 n n P2 O6P THP sing 279 n n P2 O5' THP sing 280 n n O5P HOP5 THP sing 281 n n O6P HOP6 THP sing 282 n n P1 O1P THP doub 283 n n P1 O2P THP sing 284 n n P1 O3P THP sing 285 n n P1 O3' THP sing 286 n n O2P HOP2 THP sing 287 n n O3P HOP3 THP sing 288 n n O5' C5' THP sing 289 n n C5' C4' THP sing 290 n n C5' "H5'1" THP sing 291 n n C5' "H5'2" THP sing 292 n n C4' O4' THP sing 293 n n C4' C3' THP sing 294 n n C4' H4' THP sing 295 n n O4' C1' THP sing 296 n n C3' O3' THP sing 297 n n C3' C2' THP sing 298 n n C3' H3' THP sing 299 n n C2' C1' THP sing 300 n n C2' "H2'1" THP sing 301 n n C2' "H2'2" THP sing 302 n n C1' N1 THP sing 303 n n C1' H1' THP sing 304 n n N1 C2 THP sing 305 n n N1 C6 THP sing 306 n n C2 O2 THP doub 307 n n C2 N3 THP sing 308 n n N3 C4 THP sing 309 n n N3 H3 THP sing 310 n n C4 O4 THP doub 311 n n C4 C5 THP sing 312 n n C5 C5M THP sing 313 n n C5 C6 THP doub 314 n n C5M H51 THP sing 315 n n C5M H52 THP sing 316 n n C5M H53 THP sing 317 n n C6 H6 THP sing 318 n n # _atom_sites.entry_id 5DAU _atom_sites.fract_transf_matrix[1][1] 0.032074 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001973 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016569 _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] 0.026074 _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 CA A 1 201 1 CA CA . C 3 THP A 1 202 1 THP THP . D 4 HOH A 1 301 148 HOH HOH . D 4 HOH A 2 302 116 HOH HOH . D 4 HOH A 3 303 90 HOH HOH . D 4 HOH A 4 304 92 HOH HOH . D 4 HOH A 5 305 75 HOH HOH . D 4 HOH A 6 306 5 HOH HOH . D 4 HOH A 7 307 81 HOH HOH . D 4 HOH A 8 308 16 HOH HOH . D 4 HOH A 9 309 22 HOH HOH . D 4 HOH A 10 310 117 HOH HOH . D 4 HOH A 11 311 103 HOH HOH . D 4 HOH A 12 312 121 HOH HOH . D 4 HOH A 13 313 24 HOH HOH . D 4 HOH A 14 314 134 HOH HOH . D 4 HOH A 15 315 109 HOH HOH . D 4 HOH A 16 316 101 HOH HOH . D 4 HOH A 17 317 83 HOH HOH . D 4 HOH A 18 318 8 HOH HOH . D 4 HOH A 19 319 36 HOH HOH . D 4 HOH A 20 320 9 HOH HOH . D 4 HOH A 21 321 18 HOH HOH . D 4 HOH A 22 322 126 HOH HOH . D 4 HOH A 23 323 112 HOH HOH . D 4 HOH A 24 324 93 HOH HOH . D 4 HOH A 25 325 42 HOH HOH . D 4 HOH A 26 326 137 HOH HOH . D 4 HOH A 27 327 25 HOH HOH . D 4 HOH A 28 328 1 HOH HOH . D 4 HOH A 29 329 107 HOH HOH . D 4 HOH A 30 330 6 HOH HOH . D 4 HOH A 31 331 46 HOH HOH . D 4 HOH A 32 332 129 HOH HOH . D 4 HOH A 33 333 128 HOH HOH . D 4 HOH A 34 334 76 HOH HOH . D 4 HOH A 35 335 72 HOH HOH . D 4 HOH A 36 336 62 HOH HOH . D 4 HOH A 37 337 143 HOH HOH . D 4 HOH A 38 338 15 HOH HOH . D 4 HOH A 39 339 10 HOH HOH . D 4 HOH A 40 340 51 HOH HOH . D 4 HOH A 41 341 102 HOH HOH . D 4 HOH A 42 342 28 HOH HOH . D 4 HOH A 43 343 32 HOH HOH . D 4 HOH A 44 344 23 HOH HOH . D 4 HOH A 45 345 113 HOH HOH . D 4 HOH A 46 346 19 HOH HOH . D 4 HOH A 47 347 59 HOH HOH . D 4 HOH A 48 348 105 HOH HOH . D 4 HOH A 49 349 66 HOH HOH . D 4 HOH A 50 350 61 HOH HOH . D 4 HOH A 51 351 145 HOH HOH . D 4 HOH A 52 352 44 HOH HOH . D 4 HOH A 53 353 106 HOH HOH . D 4 HOH A 54 354 35 HOH HOH . D 4 HOH A 55 355 56 HOH HOH . D 4 HOH A 56 356 67 HOH HOH . D 4 HOH A 57 357 85 HOH HOH . D 4 HOH A 58 358 58 HOH HOH . D 4 HOH A 59 359 13 HOH HOH . D 4 HOH A 60 360 4 HOH HOH . D 4 HOH A 61 361 110 HOH HOH . D 4 HOH A 62 362 136 HOH HOH . D 4 HOH A 63 363 138 HOH HOH . D 4 HOH A 64 364 29 HOH HOH . D 4 HOH A 65 365 30 HOH HOH . D 4 HOH A 66 366 142 HOH HOH . D 4 HOH A 67 367 77 HOH HOH . D 4 HOH A 68 368 49 HOH HOH . D 4 HOH A 69 369 43 HOH HOH . D 4 HOH A 70 370 54 HOH HOH . D 4 HOH A 71 371 21 HOH HOH . D 4 HOH A 72 372 45 HOH HOH . D 4 HOH A 73 373 123 HOH HOH . D 4 HOH A 74 374 26 HOH HOH . D 4 HOH A 75 375 88 HOH HOH . D 4 HOH A 76 376 73 HOH HOH . D 4 HOH A 77 377 39 HOH HOH . D 4 HOH A 78 378 89 HOH HOH . D 4 HOH A 79 379 63 HOH HOH . D 4 HOH A 80 380 2 HOH HOH . D 4 HOH A 81 381 50 HOH HOH . D 4 HOH A 82 382 114 HOH HOH . D 4 HOH A 83 383 140 HOH HOH . D 4 HOH A 84 384 95 HOH HOH . D 4 HOH A 85 385 79 HOH HOH . D 4 HOH A 86 386 96 HOH HOH . D 4 HOH A 87 387 98 HOH HOH . D 4 HOH A 88 388 55 HOH HOH . D 4 HOH A 89 389 130 HOH HOH . D 4 HOH A 90 390 64 HOH HOH . D 4 HOH A 91 391 38 HOH HOH . D 4 HOH A 92 392 71 HOH HOH . D 4 HOH A 93 393 104 HOH HOH . D 4 HOH A 94 394 119 HOH HOH . D 4 HOH A 95 395 146 HOH HOH . D 4 HOH A 96 396 65 HOH HOH . D 4 HOH A 97 397 151 HOH HOH . D 4 HOH A 98 398 68 HOH HOH . D 4 HOH A 99 399 47 HOH HOH . D 4 HOH A 100 400 37 HOH HOH . D 4 HOH A 101 401 74 HOH HOH . D 4 HOH A 102 402 149 HOH HOH . D 4 HOH A 103 403 40 HOH HOH . D 4 HOH A 104 404 144 HOH HOH . D 4 HOH A 105 405 125 HOH HOH . D 4 HOH A 106 406 99 HOH HOH . D 4 HOH A 107 407 108 HOH HOH . D 4 HOH A 108 408 60 HOH HOH . D 4 HOH A 109 409 27 HOH HOH . D 4 HOH A 110 410 53 HOH HOH . D 4 HOH A 111 411 135 HOH HOH . D 4 HOH A 112 412 91 HOH HOH . D 4 HOH A 113 413 115 HOH HOH . D 4 HOH A 114 414 31 HOH HOH . D 4 HOH A 115 415 84 HOH HOH . D 4 HOH A 116 416 86 HOH HOH . D 4 HOH A 117 417 82 HOH HOH . D 4 HOH A 118 418 139 HOH HOH . D 4 HOH A 119 419 111 HOH HOH . D 4 HOH A 120 420 17 HOH HOH . D 4 HOH A 121 421 7 HOH HOH . D 4 HOH A 122 422 41 HOH HOH . D 4 HOH A 123 423 80 HOH HOH . D 4 HOH A 124 424 48 HOH HOH . D 4 HOH A 125 425 69 HOH HOH . D 4 HOH A 126 426 3 HOH HOH . D 4 HOH A 127 427 127 HOH HOH . D 4 HOH A 128 428 78 HOH HOH . D 4 HOH A 129 429 70 HOH HOH . D 4 HOH A 130 430 124 HOH HOH . D 4 HOH A 131 431 120 HOH HOH . D 4 HOH A 132 432 131 HOH HOH . D 4 HOH A 133 433 133 HOH HOH . D 4 HOH A 134 434 57 HOH HOH . D 4 HOH A 135 435 150 HOH HOH . D 4 HOH A 136 436 122 HOH HOH . D 4 HOH A 137 437 100 HOH HOH . D 4 HOH A 138 438 147 HOH HOH . D 4 HOH A 139 439 94 HOH HOH . D 4 HOH A 140 440 97 HOH HOH . D 4 HOH A 141 441 34 HOH HOH . D 4 HOH A 142 442 33 HOH HOH . D 4 HOH A 143 443 12 HOH HOH . D 4 HOH A 144 444 11 HOH HOH . D 4 HOH A 145 445 14 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 P2 THP . . . C 3 15.572 11.228 43.123 1 8.66 ? P2 THP 202 A 1 HETATM 2 O O4P THP . . . C 3 15.542 9.744 43.415 1 8.93 ? O4P THP 202 A 1 HETATM 3 O O5P THP . . . C 3 16.845 11.92 43.606 1 11.48 ? O5P THP 202 A 1 HETATM 4 O O6P THP . . . C 3 14.335 11.958 43.594 1 10.05 ? O6P THP 202 A 1 HETATM 5 P P1 THP . . . C 3 18.88 14.671 39.262 1 11.23 ? P1 THP 202 A 1 HETATM 6 O O1P THP . . . C 3 19.837 15.258 38.26 1 13.97 ? O1P THP 202 A 1 HETATM 7 O O2P THP . . . C 3 19.542 13.504 40.006 1 12.66 ? O2P THP 202 A 1 HETATM 8 O O3P THP . . . C 3 18.151 15.629 40.129 1 12.53 ? O3P THP 202 A 1 HETATM 9 O O5' THP . . . C 3 15.565 11.28 41.557 1 8.78 ? O5' THP 202 A 1 HETATM 10 C C5' THP . . . C 3 15.583 12.536 40.834 1 10.32 ? C5' THP 202 A 1 HETATM 11 C C4' THP . . . C 3 16.532 12.403 39.677 1 9.62 ? C4' THP 202 A 1 HETATM 12 O O4' THP . . . C 3 16.146 11.327 38.844 1 9.32 ? O4' THP 202 A 1 HETATM 13 C C3' THP . . . C 3 16.487 13.633 38.775 1 10.44 ? C3' THP 202 A 1 HETATM 14 O O3' THP . . . C 3 17.804 13.98 38.284 1 10.9 ? O3' THP 202 A 1 HETATM 15 C C2' THP . . . C 3 15.585 13.227 37.612 1 9.73 ? C2' THP 202 A 1 HETATM 16 C C1' THP . . . C 3 15.797 11.714 37.526 1 9.45 ? C1' THP 202 A 1 HETATM 17 N N1 THP . . . C 3 14.541 11.054 37.114 1 8.64 ? N1 THP 202 A 1 HETATM 18 C C2 THP . . . C 3 14.323 10.828 35.766 1 10.22 ? C2 THP 202 A 1 HETATM 19 O O2 THP . . . C 3 15.225 11.158 34.927 1 12.31 ? O2 THP 202 A 1 HETATM 20 N N3 THP . . . C 3 13.177 10.299 35.346 1 8.86 ? N3 THP 202 A 1 HETATM 21 C C4 THP . . . C 3 12.166 10.053 36.197 1 9.31 ? C4 THP 202 A 1 HETATM 22 O O4 THP . . . C 3 11.083 9.632 35.733 1 9.37 ? O4 THP 202 A 1 HETATM 23 C C5 THP . . . C 3 12.367 10.248 37.632 1 7.25 ? C5 THP 202 A 1 HETATM 24 C C5M THP . . . C 3 11.296 9.91 38.623 1 8.24 ? C5M THP 202 A 1 HETATM 25 C C6 THP . . . C 3 13.574 10.797 38.027 1 7.89 ? C6 THP 202 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #