data_4O7W
#
_model_server_result.job_id            LXgTG6a-pXv7Q7b95N0Mqg 
_model_server_result.datetime_utc      '2025-07-31 10:07:33' 
_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          4o7w 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    4O7W 
#
_exptl.entry_id    4O7W 
_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            4O7W 
_cell.length_a            44.15 
_cell.length_b            154.53 
_cell.length_c            78.43 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4O7W 
_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_654 -x+1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 44.15 0 -39.215 
#
_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 393 n n 
PA O2A TYD sing 394 n n 
PA O3A TYD sing 395 n n 
PA O5' TYD sing 396 n n 
O2A HOA2 TYD sing 397 n n 
O3A PB TYD sing 398 n n 
PB O1B TYD doub 399 n n 
PB O2B TYD sing 400 n n 
PB O3B TYD sing 401 n n 
O2B HOB2 TYD sing 402 n n 
O3B HOB3 TYD sing 403 n n 
O5' C5' TYD sing 404 n n 
C5' C4' TYD sing 405 n n 
C5' "H5'1" TYD sing 406 n n 
C5' "H5'2" TYD sing 407 n n 
C4' O4' TYD sing 408 n n 
C4' C3' TYD sing 409 n n 
C4' H4' TYD sing 410 n n 
O4' C1' TYD sing 411 n n 
C3' O3' TYD sing 412 n n 
C3' C2' TYD sing 413 n n 
C3' H3' TYD sing 414 n n 
O3' HO3' TYD sing 415 n n 
C2' C1' TYD sing 416 n n 
C2' "H2'1" TYD sing 417 n n 
C2' "H2'2" TYD sing 418 n n 
C1' N1 TYD sing 419 n n 
C1' H1' TYD sing 420 n n 
N1 C2 TYD sing 421 n y 
N1 C6 TYD sing 422 n y 
C2 O2 TYD doub 423 n n 
C2 N3 TYD sing 424 n y 
N3 C4 TYD sing 425 n y 
N3 HN3 TYD sing 426 n n 
C4 O4 TYD doub 427 n n 
C4 C5 TYD sing 428 n y 
C5 C5M TYD sing 429 n n 
C5 C6 TYD doub 430 n y 
C5M H51 TYD sing 431 n n 
C5M H52 TYD sing 432 n n 
C5M H53 TYD sing 433 n n 
C6 H6 TYD sing 434 n n 
#
_atom_sites.entry_id                     4O7W 
_atom_sites.fract_transf_matrix[1][1]    0.02265 
_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]    0.006471 
_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]    0.01275 
_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 ATP A 1 302 422 ATP ATP . 
D 4 PO4 A 1 303 501 PO4 PO4 . 
E 5 ACT A 1 304 502 ACT ACT . 
F 6 HOH A 1 401 295 HOH HOH . 
F 6 HOH A 2 402 296 HOH HOH . 
F 6 HOH A 3 403 297 HOH HOH . 
F 6 HOH A 4 404 298 HOH HOH . 
F 6 HOH A 5 405 299 HOH HOH . 
F 6 HOH A 6 406 300 HOH HOH . 
F 6 HOH A 7 407 301 HOH HOH . 
F 6 HOH A 8 408 302 HOH HOH . 
F 6 HOH A 9 409 303 HOH HOH . 
F 6 HOH A 10 410 304 HOH HOH . 
F 6 HOH A 11 411 305 HOH HOH . 
F 6 HOH A 12 412 306 HOH HOH . 
F 6 HOH A 13 413 307 HOH HOH . 
F 6 HOH A 14 414 308 HOH HOH . 
F 6 HOH A 15 415 309 HOH HOH . 
F 6 HOH A 16 416 310 HOH HOH . 
F 6 HOH A 17 417 311 HOH HOH . 
F 6 HOH A 18 418 312 HOH HOH . 
F 6 HOH A 19 419 313 HOH HOH . 
F 6 HOH A 20 420 314 HOH HOH . 
F 6 HOH A 21 421 315 HOH HOH . 
F 6 HOH A 22 422 316 HOH HOH . 
F 6 HOH A 23 423 317 HOH HOH . 
F 6 HOH A 24 424 318 HOH HOH . 
F 6 HOH A 25 425 319 HOH HOH . 
F 6 HOH A 26 426 320 HOH HOH . 
F 6 HOH A 27 427 321 HOH HOH . 
F 6 HOH A 28 428 322 HOH HOH . 
F 6 HOH A 29 429 323 HOH HOH . 
F 6 HOH A 30 430 324 HOH HOH . 
F 6 HOH A 31 431 325 HOH HOH . 
F 6 HOH A 32 432 326 HOH HOH . 
F 6 HOH A 33 433 327 HOH HOH . 
F 6 HOH A 34 434 328 HOH HOH . 
F 6 HOH A 35 435 329 HOH HOH . 
F 6 HOH A 36 436 330 HOH HOH . 
F 6 HOH A 37 437 331 HOH HOH . 
F 6 HOH A 38 438 332 HOH HOH . 
F 6 HOH A 39 439 333 HOH HOH . 
F 6 HOH A 40 440 334 HOH HOH . 
F 6 HOH A 41 441 335 HOH HOH . 
F 6 HOH A 42 442 336 HOH HOH . 
F 6 HOH A 43 443 337 HOH HOH . 
F 6 HOH A 44 444 338 HOH HOH . 
F 6 HOH A 45 445 339 HOH HOH . 
F 6 HOH A 46 446 340 HOH HOH . 
F 6 HOH A 47 447 341 HOH HOH . 
F 6 HOH A 48 448 342 HOH HOH . 
F 6 HOH A 49 449 343 HOH HOH . 
F 6 HOH A 50 450 344 HOH HOH . 
F 6 HOH A 51 451 345 HOH HOH . 
F 6 HOH A 52 452 346 HOH HOH . 
F 6 HOH A 53 453 347 HOH HOH . 
F 6 HOH A 54 454 348 HOH HOH . 
F 6 HOH A 55 455 349 HOH HOH . 
F 6 HOH A 56 456 350 HOH HOH . 
F 6 HOH A 57 457 351 HOH HOH . 
F 6 HOH A 58 458 352 HOH HOH . 
F 6 HOH A 59 459 353 HOH HOH . 
F 6 HOH A 60 460 354 HOH HOH . 
F 6 HOH A 61 461 355 HOH HOH . 
F 6 HOH A 62 462 356 HOH HOH . 
F 6 HOH A 63 463 357 HOH HOH . 
F 6 HOH A 64 464 358 HOH HOH . 
F 6 HOH A 65 465 359 HOH HOH . 
F 6 HOH A 66 466 360 HOH HOH . 
F 6 HOH A 67 467 361 HOH HOH . 
F 6 HOH A 68 468 362 HOH HOH . 
F 6 HOH A 69 469 363 HOH HOH . 
F 6 HOH A 70 470 364 HOH HOH . 
F 6 HOH A 71 471 365 HOH HOH . 
F 6 HOH A 72 472 366 HOH HOH . 
F 6 HOH A 73 473 367 HOH HOH . 
F 6 HOH A 74 474 368 HOH HOH . 
F 6 HOH A 75 475 369 HOH HOH . 
F 6 HOH A 76 476 370 HOH HOH . 
F 6 HOH A 77 477 371 HOH HOH . 
F 6 HOH A 78 478 372 HOH HOH . 
F 6 HOH A 79 479 373 HOH HOH . 
F 6 HOH A 80 480 374 HOH HOH . 
F 6 HOH A 81 481 375 HOH HOH . 
F 6 HOH A 82 482 376 HOH HOH . 
F 6 HOH A 83 483 377 HOH HOH . 
F 6 HOH A 84 484 378 HOH HOH . 
F 6 HOH A 85 485 379 HOH HOH . 
F 6 HOH A 86 486 380 HOH HOH . 
F 6 HOH A 87 487 381 HOH HOH . 
F 6 HOH A 88 488 382 HOH HOH . 
F 6 HOH A 89 489 383 HOH HOH . 
F 6 HOH A 90 490 384 HOH HOH . 
F 6 HOH A 91 491 385 HOH HOH . 
F 6 HOH A 92 492 386 HOH HOH . 
F 6 HOH A 93 493 387 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 . . . B 2 14.265 -15.434 -10.833 0.9 17.13 ? PA TYD 301 A 1 
HETATM 2 O O1A TYD . . . B 2 12.929 -15.237 -11.482 0.9 16.78 ? O1A TYD 301 A 1 
HETATM 3 O O2A TYD . . . B 2 15.291 -16.189 -11.652 0.9 17.52 ? O2A TYD 301 A 1 
HETATM 4 O O3A TYD . . . B 2 14.986 -14.061 -10.419 0.9 20.37 ? O3A TYD 301 A 1 
HETATM 5 P PB TYD . . . B 2 14.37 -12.735 -9.735 0.9 23.37 ? PB TYD 301 A 1 
HETATM 6 O O1B TYD . . . B 2 13 -12.522 -10.339 0.9 24.25 ? O1B TYD 301 A 1 
HETATM 7 O O2B TYD . . . B 2 14.293 -13.077 -8.262 0.9 25.91 ? O2B TYD 301 A 1 
HETATM 8 O O3B TYD . . . B 2 15.413 -11.701 -10.041 0.9 24.05 ? O3B TYD 301 A 1 
HETATM 9 O O5' TYD . . . B 2 14.029 -16.149 -9.429 0.9 16.85 ? O5' TYD 301 A 1 
HETATM 10 C C5' TYD . . . B 2 13.479 -17.455 -9.387 0.9 16.26 ? C5' TYD 301 A 1 
HETATM 11 C C4' TYD . . . B 2 13.148 -17.883 -7.956 0.9 16.9 ? C4' TYD 301 A 1 
HETATM 12 O O4' TYD . . . B 2 14.357 -18.245 -7.29 0.9 16.91 ? O4' TYD 301 A 1 
HETATM 13 C C3' TYD . . . B 2 12.48 -16.801 -7.101 0.9 16.61 ? C3' TYD 301 A 1 
HETATM 14 O O3' TYD . . . B 2 11.584 -17.452 -6.206 0.9 15.41 ? O3' TYD 301 A 1 
HETATM 15 C C2' TYD . . . B 2 13.598 -16.207 -6.275 0.9 17.21 ? C2' TYD 301 A 1 
HETATM 16 C C1' TYD . . . B 2 14.601 -17.354 -6.191 0.9 17.83 ? C1' TYD 301 A 1 
HETATM 17 N N1 TYD . . . B 2 15.993 -16.896 -6.27 0.9 19.58 ? N1 TYD 301 A 1 
HETATM 18 C C2 TYD . . . B 2 16.657 -16.414 -5.101 0.9 18.96 ? C2 TYD 301 A 1 
HETATM 19 O O2 TYD . . . B 2 16.061 -16.379 -4.011 0.9 16.71 ? O2 TYD 301 A 1 
HETATM 20 N N3 TYD . . . B 2 17.935 -16.009 -5.163 0.9 20.66 ? N3 TYD 301 A 1 
HETATM 21 C C4 TYD . . . B 2 18.616 -16.069 -6.328 0.9 22.27 ? C4 TYD 301 A 1 
HETATM 22 O O4 TYD . . . B 2 19.803 -15.709 -6.378 0.9 24.59 ? O4 TYD 301 A 1 
HETATM 23 C C5 TYD . . . B 2 17.966 -16.587 -7.567 0.9 22.19 ? C5 TYD 301 A 1 
HETATM 24 C C5M TYD . . . B 2 18.703 -16.672 -8.892 0.9 22.37 ? C5M TYD 301 A 1 
HETATM 25 C C6 TYD . . . B 2 16.639 -16.985 -7.455 0.9 20.72 ? C6 TYD 301 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           352 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           25 
#