data_1TSD # _model_server_result.job_id 8O6-ElBLRypQULt8SP2xoQ _model_server_result.datetime_utc '2025-02-27 01:52:14' _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 1tsd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":265}' # _entry.id 1TSD # _exptl.entry_id 1TSD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 1TSD _cell.length_a 127.52 _cell.length_b 127.52 _cell.length_c 68.25 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1TSD _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _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,G,H,I,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G N 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 covale ? covale1 A C FMT 1 A FMT 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 B C FMT 1 B FMT 0 1_555 B N MET 2 B MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # _atom_sites.entry_id 1TSD _atom_sites.fract_transf_matrix[1][1] 0.007842 _atom_sites.fract_transf_matrix[1][2] 0.004528 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009055 _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] 0.014652 _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 C 2 BME A 1 265 3 BME BME . D 2 BME A 1 266 4 BME BME . E 3 UMP A 1 267 1 UMP UMP . F 4 F89 A 1 268 2 F89 U18 . G 3 UMP B 1 265 1 UMP UMP . H 4 F89 B 1 266 2 F89 U18 . I 5 HOH A 1 271 271 HOH HOH . I 5 HOH A 2 272 272 HOH HOH . I 5 HOH A 3 273 273 HOH HOH . I 5 HOH A 4 275 275 HOH HOH . I 5 HOH A 5 276 276 HOH HOH . I 5 HOH A 6 277 277 HOH HOH . I 5 HOH A 7 279 279 HOH HOH . I 5 HOH A 8 281 281 HOH HOH . I 5 HOH A 9 282 282 HOH HOH . I 5 HOH A 10 286 286 HOH HOH . I 5 HOH A 11 289 289 HOH HOH . I 5 HOH A 12 290 290 HOH HOH . I 5 HOH A 13 291 291 HOH HOH . I 5 HOH A 14 293 293 HOH HOH . I 5 HOH A 15 294 294 HOH HOH . I 5 HOH A 16 295 295 HOH HOH . I 5 HOH A 17 296 296 HOH HOH . I 5 HOH A 18 297 297 HOH HOH . I 5 HOH A 19 299 299 HOH HOH . I 5 HOH A 20 301 301 HOH HOH . I 5 HOH A 21 302 302 HOH HOH . I 5 HOH A 22 303 303 HOH HOH . I 5 HOH A 23 307 307 HOH HOH . I 5 HOH A 24 308 308 HOH HOH . I 5 HOH A 25 309 309 HOH HOH . I 5 HOH A 26 310 310 HOH HOH . I 5 HOH A 27 311 311 HOH HOH . I 5 HOH A 28 312 312 HOH HOH . I 5 HOH A 29 313 313 HOH HOH . I 5 HOH A 30 314 314 HOH HOH . I 5 HOH A 31 315 315 HOH HOH . I 5 HOH A 32 316 316 HOH HOH . I 5 HOH A 33 317 317 HOH HOH . I 5 HOH A 34 320 320 HOH HOH . I 5 HOH A 35 323 323 HOH HOH . I 5 HOH A 36 324 324 HOH HOH . I 5 HOH A 37 326 326 HOH HOH . I 5 HOH A 38 333 333 HOH HOH . I 5 HOH A 39 335 335 HOH HOH . I 5 HOH A 40 336 336 HOH HOH . I 5 HOH A 41 337 337 HOH HOH . I 5 HOH A 42 338 338 HOH HOH . I 5 HOH A 43 340 340 HOH HOH . I 5 HOH A 44 342 342 HOH HOH . I 5 HOH A 45 343 343 HOH HOH . I 5 HOH A 46 344 344 HOH HOH . I 5 HOH A 47 345 345 HOH HOH . I 5 HOH A 48 346 346 HOH HOH . I 5 HOH A 49 347 347 HOH HOH . I 5 HOH A 50 348 348 HOH HOH . I 5 HOH A 51 349 349 HOH HOH . I 5 HOH A 52 350 350 HOH HOH . I 5 HOH A 53 351 351 HOH HOH . I 5 HOH A 54 352 352 HOH HOH . I 5 HOH A 55 353 353 HOH HOH . I 5 HOH A 56 355 355 HOH HOH . I 5 HOH A 57 356 356 HOH HOH . I 5 HOH A 58 357 357 HOH HOH . I 5 HOH A 59 359 359 HOH HOH . I 5 HOH A 60 360 360 HOH HOH . I 5 HOH A 61 361 361 HOH HOH . I 5 HOH A 62 364 364 HOH HOH . I 5 HOH A 63 365 365 HOH HOH . I 5 HOH A 64 366 366 HOH HOH . I 5 HOH A 65 367 367 HOH HOH . I 5 HOH A 66 369 369 HOH HOH . I 5 HOH A 67 371 371 HOH HOH . I 5 HOH A 68 374 374 HOH HOH . I 5 HOH A 69 375 375 HOH HOH . I 5 HOH A 70 378 378 HOH HOH . I 5 HOH A 71 379 379 HOH HOH . I 5 HOH A 72 380 380 HOH HOH . I 5 HOH A 73 381 381 HOH HOH . I 5 HOH A 74 382 382 HOH HOH . I 5 HOH A 75 383 383 HOH HOH . I 5 HOH A 76 384 384 HOH HOH . I 5 HOH A 77 385 385 HOH HOH . I 5 HOH A 78 394 394 HOH HOH . I 5 HOH A 79 400 400 HOH HOH . I 5 HOH A 80 404 404 HOH HOH . I 5 HOH A 81 405 405 HOH HOH . I 5 HOH A 82 407 407 HOH HOH . I 5 HOH A 83 408 408 HOH HOH . I 5 HOH A 84 411 411 HOH HOH . I 5 HOH A 85 412 412 HOH HOH . I 5 HOH A 86 415 415 HOH HOH . I 5 HOH A 87 418 418 HOH HOH . I 5 HOH A 88 422 422 HOH HOH . I 5 HOH A 89 427 427 HOH HOH . I 5 HOH A 90 429 429 HOH HOH . I 5 HOH A 91 430 430 HOH HOH . I 5 HOH A 92 431 431 HOH HOH . I 5 HOH A 93 432 432 HOH HOH . I 5 HOH A 94 433 433 HOH HOH . I 5 HOH A 95 434 434 HOH HOH . I 5 HOH A 96 435 435 HOH HOH . I 5 HOH A 97 437 437 HOH HOH . I 5 HOH A 98 440 440 HOH HOH . I 5 HOH A 99 441 441 HOH HOH . I 5 HOH A 100 442 442 HOH HOH . I 5 HOH A 101 443 443 HOH HOH . I 5 HOH A 102 444 444 HOH HOH . I 5 HOH A 103 447 447 HOH HOH . I 5 HOH A 104 449 449 HOH HOH . I 5 HOH A 105 450 450 HOH HOH . I 5 HOH A 106 451 451 HOH HOH . I 5 HOH A 107 452 452 HOH HOH . I 5 HOH A 108 457 457 HOH HOH . J 5 HOH B 1 270 270 HOH HOH . J 5 HOH B 2 274 274 HOH HOH . J 5 HOH B 3 278 278 HOH HOH . J 5 HOH B 4 280 280 HOH HOH . J 5 HOH B 5 283 283 HOH HOH . J 5 HOH B 6 284 284 HOH HOH . J 5 HOH B 7 285 285 HOH HOH . J 5 HOH B 8 287 287 HOH HOH . J 5 HOH B 9 288 288 HOH HOH . J 5 HOH B 10 292 292 HOH HOH . J 5 HOH B 11 298 298 HOH HOH . J 5 HOH B 12 300 300 HOH HOH . J 5 HOH B 13 304 304 HOH HOH . J 5 HOH B 14 305 305 HOH HOH . J 5 HOH B 15 306 306 HOH HOH . J 5 HOH B 16 318 318 HOH HOH . J 5 HOH B 17 319 319 HOH HOH . J 5 HOH B 18 321 321 HOH HOH . J 5 HOH B 19 322 322 HOH HOH . J 5 HOH B 20 325 325 HOH HOH . J 5 HOH B 21 327 327 HOH HOH . J 5 HOH B 22 328 328 HOH HOH . J 5 HOH B 23 329 329 HOH HOH . J 5 HOH B 24 330 330 HOH HOH . J 5 HOH B 25 331 331 HOH HOH . J 5 HOH B 26 332 332 HOH HOH . J 5 HOH B 27 334 334 HOH HOH . J 5 HOH B 28 339 339 HOH HOH . J 5 HOH B 29 341 341 HOH HOH . J 5 HOH B 30 354 354 HOH HOH . J 5 HOH B 31 358 358 HOH HOH . J 5 HOH B 32 362 362 HOH HOH . J 5 HOH B 33 363 363 HOH HOH . J 5 HOH B 34 368 368 HOH HOH . J 5 HOH B 35 370 370 HOH HOH . J 5 HOH B 36 372 372 HOH HOH . J 5 HOH B 37 373 373 HOH HOH . J 5 HOH B 38 376 376 HOH HOH . J 5 HOH B 39 377 377 HOH HOH . J 5 HOH B 40 386 386 HOH HOH . J 5 HOH B 41 387 387 HOH HOH . J 5 HOH B 42 388 388 HOH HOH . J 5 HOH B 43 389 389 HOH HOH . J 5 HOH B 44 390 390 HOH HOH . J 5 HOH B 45 391 391 HOH HOH . J 5 HOH B 46 392 392 HOH HOH . J 5 HOH B 47 393 393 HOH HOH . J 5 HOH B 48 395 395 HOH HOH . J 5 HOH B 49 396 396 HOH HOH . J 5 HOH B 50 397 397 HOH HOH . J 5 HOH B 51 398 398 HOH HOH . J 5 HOH B 52 399 399 HOH HOH . J 5 HOH B 53 401 401 HOH HOH . J 5 HOH B 54 402 402 HOH HOH . J 5 HOH B 55 403 403 HOH HOH . J 5 HOH B 56 406 406 HOH HOH . J 5 HOH B 57 409 409 HOH HOH . J 5 HOH B 58 410 410 HOH HOH . J 5 HOH B 59 413 413 HOH HOH . J 5 HOH B 60 414 414 HOH HOH . J 5 HOH B 61 416 416 HOH HOH . J 5 HOH B 62 417 417 HOH HOH . J 5 HOH B 63 419 419 HOH HOH . J 5 HOH B 64 420 420 HOH HOH . J 5 HOH B 65 421 421 HOH HOH . J 5 HOH B 66 423 423 HOH HOH . J 5 HOH B 67 424 424 HOH HOH . J 5 HOH B 68 425 425 HOH HOH . J 5 HOH B 69 426 426 HOH HOH . J 5 HOH B 70 428 428 HOH HOH . J 5 HOH B 71 436 436 HOH HOH . J 5 HOH B 72 438 438 HOH HOH . J 5 HOH B 73 439 439 HOH HOH . J 5 HOH B 74 445 445 HOH HOH . J 5 HOH B 75 446 446 HOH HOH . J 5 HOH B 76 448 448 HOH HOH . J 5 HOH B 77 453 453 HOH HOH . J 5 HOH B 78 454 454 HOH HOH . J 5 HOH B 79 455 455 HOH HOH . J 5 HOH B 80 456 456 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 N N1 UMP . . . G 3 44.606 34.311 24.807 1 29.2 ? N1 UMP 265 B 1 HETATM 2 C C2 UMP . . . G 3 43.735 35.288 25.309 1 26.69 ? C2 UMP 265 B 1 HETATM 3 N N3 UMP . . . G 3 42.831 35.882 24.519 1 27.65 ? N3 UMP 265 B 1 HETATM 4 C C4 UMP . . . G 3 42.657 35.619 23.181 1 30.61 ? C4 UMP 265 B 1 HETATM 5 C C5 UMP . . . G 3 43.595 34.639 22.649 1 30.14 ? C5 UMP 265 B 1 HETATM 6 C C6 UMP . . . G 3 44.484 34.065 23.502 1 29.41 ? C6 UMP 265 B 1 HETATM 7 O O2 UMP . . . G 3 43.712 35.577 26.4 1 25.78 ? O2 UMP 265 B 1 HETATM 8 O O4 UMP . . . G 3 41.82 36.131 22.443 1 33.84 ? O4 UMP 265 B 1 HETATM 9 C C1' UMP . . . G 3 45.572 33.659 25.435 1 27.97 ? C1' UMP 265 B 1 HETATM 10 C C2' UMP . . . G 3 45.308 32.483 26.484 1 26.5 ? C2' UMP 265 B 1 HETATM 11 C C3' UMP . . . G 3 46.723 31.883 26.57 1 27.75 ? C3' UMP 265 B 1 HETATM 12 C C4' UMP . . . G 3 47.082 31.825 25.069 1 28.3 ? C4' UMP 265 B 1 HETATM 13 O O3' UMP . . . G 3 47.605 32.795 27.171 1 27.99 ? O3' UMP 265 B 1 HETATM 14 O O4' UMP . . . G 3 46.592 33.101 24.507 1 27.44 ? O4' UMP 265 B 1 HETATM 15 C C5' UMP . . . G 3 46.614 30.702 24.319 1 28.44 ? C5' UMP 265 B 1 HETATM 16 O O5' UMP . . . G 3 47.235 29.571 24.462 1 27.92 ? O5' UMP 265 B 1 HETATM 17 P P UMP . . . G 3 46.686 28.132 24.624 1 25.03 ? P UMP 265 B 1 HETATM 18 O OP1 UMP . . . G 3 45.739 28.302 25.819 1 26.69 ? OP1 UMP 265 B 1 HETATM 19 O OP2 UMP . . . G 3 46.042 27.673 23.305 1 23.88 ? OP2 UMP 265 B 1 HETATM 20 O OP3 UMP . . . G 3 47.857 27.196 25.041 1 25.99 ? OP3 UMP 265 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #