data_4O7S # _model_server_result.job_id '_Elet3p_efNHtNi8hj4iTw' _model_server_result.datetime_utc '2025-07-17 03:44:07' _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 4o7s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4O7S # _exptl.entry_id 4O7S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-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 4O7S _cell.length_a 43.89 _cell.length_b 154.43 _cell.length_c 78.1 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4O7S _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,D,E,F _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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 43.89 0 39.05 # _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 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-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 PA O1A TYD doub 381 n n PA O2A TYD sing 382 n n PA O3A TYD sing 383 n n PA O5' TYD sing 384 n n O2A HOA2 TYD sing 385 n n O3A PB TYD sing 386 n n PB O1B TYD doub 387 n n PB O2B TYD sing 388 n n PB O3B TYD sing 389 n n O2B HOB2 TYD sing 390 n n O3B HOB3 TYD sing 391 n n O5' C5' TYD sing 392 n n C5' C4' TYD sing 393 n n C5' "H5'1" TYD sing 394 n n C5' "H5'2" TYD sing 395 n n C4' O4' TYD sing 396 n n C4' C3' TYD sing 397 n n C4' H4' TYD sing 398 n n O4' C1' TYD sing 399 n n C3' O3' TYD sing 400 n n C3' C2' TYD sing 401 n n C3' H3' TYD sing 402 n n O3' HO3' TYD sing 403 n n C2' C1' TYD sing 404 n n C2' "H2'1" TYD sing 405 n n C2' "H2'2" TYD sing 406 n n C1' N1 TYD sing 407 n n C1' H1' TYD sing 408 n n N1 C2 TYD sing 409 n y N1 C6 TYD sing 410 n y C2 O2 TYD doub 411 n n C2 N3 TYD sing 412 n y N3 C4 TYD sing 413 n y N3 HN3 TYD sing 414 n n C4 O4 TYD doub 415 n n C4 C5 TYD sing 416 n y C5 C5M TYD sing 417 n n C5 C6 TYD doub 418 n y C5M H51 TYD sing 419 n n C5M H52 TYD sing 420 n n C5M H53 TYD sing 421 n n C6 H6 TYD sing 422 n n # _atom_sites.entry_id 4O7S _atom_sites.fract_transf_matrix[1][1] 0.022784 _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] 0.006475 _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] 0.012804 _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 TYD A 1 301 420 TYD TYD . C 3 TMP A 1 302 430 TMP TMP . D 4 PO4 A 1 303 501 PO4 PO4 . E 5 ACT A 1 304 502 ACT ACT . F 6 HOH A 1 401 301 HOH HOH . F 6 HOH A 2 402 302 HOH HOH . F 6 HOH A 3 403 303 HOH HOH . F 6 HOH A 4 404 304 HOH HOH . F 6 HOH A 5 405 305 HOH HOH . F 6 HOH A 6 406 306 HOH HOH . F 6 HOH A 7 407 307 HOH HOH . F 6 HOH A 8 408 308 HOH HOH . F 6 HOH A 9 409 309 HOH HOH . F 6 HOH A 10 410 310 HOH HOH . F 6 HOH A 11 411 311 HOH HOH . F 6 HOH A 12 412 312 HOH HOH . F 6 HOH A 13 413 313 HOH HOH . F 6 HOH A 14 414 314 HOH HOH . F 6 HOH A 15 415 315 HOH HOH . F 6 HOH A 16 416 316 HOH HOH . F 6 HOH A 17 417 317 HOH HOH . F 6 HOH A 18 418 318 HOH HOH . F 6 HOH A 19 419 319 HOH HOH . F 6 HOH A 20 420 320 HOH HOH . F 6 HOH A 21 421 321 HOH HOH . F 6 HOH A 22 422 322 HOH HOH . F 6 HOH A 23 423 323 HOH HOH . F 6 HOH A 24 424 324 HOH HOH . F 6 HOH A 25 425 325 HOH HOH . F 6 HOH A 26 426 326 HOH HOH . F 6 HOH A 27 427 327 HOH HOH . F 6 HOH A 28 428 328 HOH HOH . F 6 HOH A 29 429 329 HOH HOH . F 6 HOH A 30 430 330 HOH HOH . F 6 HOH A 31 431 331 HOH HOH . F 6 HOH A 32 432 332 HOH HOH . F 6 HOH A 33 433 333 HOH HOH . F 6 HOH A 34 434 334 HOH HOH . F 6 HOH A 35 435 335 HOH HOH . F 6 HOH A 36 436 336 HOH HOH . F 6 HOH A 37 437 337 HOH HOH . F 6 HOH A 38 438 338 HOH HOH . F 6 HOH A 39 439 339 HOH HOH . F 6 HOH A 40 440 340 HOH HOH . F 6 HOH A 41 441 341 HOH HOH . F 6 HOH A 42 442 342 HOH HOH . F 6 HOH A 43 443 343 HOH HOH . F 6 HOH A 44 444 344 HOH HOH . F 6 HOH A 45 445 345 HOH HOH . F 6 HOH A 46 446 346 HOH HOH . F 6 HOH A 47 447 347 HOH HOH . F 6 HOH A 48 448 348 HOH HOH . F 6 HOH A 49 449 349 HOH HOH . F 6 HOH A 50 450 350 HOH HOH . F 6 HOH A 51 451 351 HOH HOH . F 6 HOH A 52 452 352 HOH HOH . F 6 HOH A 53 453 353 HOH HOH . F 6 HOH A 54 454 354 HOH HOH . F 6 HOH A 55 455 355 HOH HOH . F 6 HOH A 56 456 356 HOH HOH . F 6 HOH A 57 457 357 HOH HOH . F 6 HOH A 58 458 358 HOH HOH . F 6 HOH A 59 459 359 HOH HOH . F 6 HOH A 60 460 360 HOH HOH . F 6 HOH A 61 461 361 HOH HOH . F 6 HOH A 62 462 362 HOH HOH . F 6 HOH A 63 463 363 HOH HOH . F 6 HOH A 64 464 364 HOH HOH . F 6 HOH A 65 465 365 HOH HOH . F 6 HOH A 66 466 366 HOH HOH . F 6 HOH A 67 467 367 HOH HOH . F 6 HOH A 68 468 368 HOH HOH . F 6 HOH A 69 469 369 HOH HOH . F 6 HOH A 70 470 370 HOH HOH . F 6 HOH A 71 471 371 HOH HOH . F 6 HOH A 72 472 372 HOH HOH . F 6 HOH A 73 473 373 HOH HOH . F 6 HOH A 74 474 374 HOH HOH . F 6 HOH A 75 475 375 HOH HOH . F 6 HOH A 76 476 376 HOH HOH . F 6 HOH A 77 477 377 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 PA TYD . A . B 2 14.181 15.268 10.738 0.55 20.93 ? PA TYD 301 A 1 HETATM 2 O O1A TYD . A . B 2 12.834 14.972 11.354 0.55 20.1 ? O1A TYD 301 A 1 HETATM 3 O O2A TYD . A . B 2 15.191 16.05 11.552 0.55 20.5 ? O2A TYD 301 A 1 HETATM 4 O O3A TYD . A . B 2 14.913 13.917 10.26 0.55 20.57 ? O3A TYD 301 A 1 HETATM 5 P PB TYD . A . B 2 14.259 12.605 9.59 0.55 20.74 ? PB TYD 301 A 1 HETATM 6 O O1B TYD . A . B 2 12.966 12.334 10.311 0.55 19.94 ? O1B TYD 301 A 1 HETATM 7 O O2B TYD . A . B 2 14.025 12.976 8.144 0.55 21.41 ? O2B TYD 301 A 1 HETATM 8 O O3B TYD . A . B 2 15.361 11.601 9.804 0.55 20.07 ? O3B TYD 301 A 1 HETATM 9 O O5' TYD . A . B 2 13.951 16.038 9.349 0.55 21.76 ? O5' TYD 301 A 1 HETATM 10 C C5' TYD . A . B 2 13.26 17.287 9.328 0.55 23.36 ? C5' TYD 301 A 1 HETATM 11 C C4' TYD . A . B 2 13.067 17.783 7.891 0.55 25.05 ? C4' TYD 301 A 1 HETATM 12 O O4' TYD . A . B 2 14.334 18.088 7.315 0.55 26.09 ? O4' TYD 301 A 1 HETATM 13 C C3' TYD . A . B 2 12.397 16.781 6.954 0.55 25.04 ? C3' TYD 301 A 1 HETATM 14 O O3' TYD . A . B 2 11.518 17.513 6.104 0.55 24.29 ? O3' TYD 301 A 1 HETATM 15 C C2' TYD . A . B 2 13.496 16.211 6.089 0.55 26.38 ? C2' TYD 301 A 1 HETATM 16 C C1' TYD . A . B 2 14.577 17.279 6.152 0.55 27.91 ? C1' TYD 301 A 1 HETATM 17 N N1 TYD . A . B 2 15.936 16.724 6.213 0.55 30.41 ? N1 TYD 301 A 1 HETATM 18 C C2 TYD . A . B 2 16.604 16.302 5.025 0.55 30.48 ? C2 TYD 301 A 1 HETATM 19 O O2 TYD . A . B 2 16.029 16.383 3.918 0.55 28.51 ? O2 TYD 301 A 1 HETATM 20 N N3 TYD . A . B 2 17.856 15.808 5.082 0.55 31.77 ? N3 TYD 301 A 1 HETATM 21 C C4 TYD . A . B 2 18.51 15.716 6.256 0.55 33.89 ? C4 TYD 301 A 1 HETATM 22 O O4 TYD . A . B 2 19.671 15.264 6.295 0.55 35.29 ? O4 TYD 301 A 1 HETATM 23 C C5 TYD . A . B 2 17.842 16.166 7.51 0.55 33.88 ? C5 TYD 301 A 1 HETATM 24 C C5M TYD . A . B 2 18.522 16.103 8.856 0.55 35.57 ? C5M TYD 301 A 1 HETATM 25 C C6 TYD . A . B 2 16.552 16.664 7.409 0.55 32.26 ? C6 TYD 301 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 25 #