data_1O25 # _model_server_result.job_id x9bSV9Q5Kb-G0e-PhUrpKQ _model_server_result.datetime_utc '2024-11-24 04:40:11' _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 1o25 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":618}' # _entry.id 1O25 # _exptl.entry_id 1O25 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 1O25 _cell.length_a 54.682 _cell.length_b 116.703 _cell.length_c 141.727 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1O25 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,K,L _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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _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 # 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 N1 C2 UMP sing 358 n n N1 C6 UMP sing 359 n n N1 C1' UMP sing 360 n n C2 N3 UMP sing 361 n n C2 O2 UMP doub 362 n n N3 C4 UMP sing 363 n n N3 HN3 UMP sing 364 n n C4 C5 UMP sing 365 n n C4 O4 UMP doub 366 n n C5 C6 UMP doub 367 n n C5 H5 UMP sing 368 n n C6 H6 UMP sing 369 n n C1' C2' UMP sing 370 n n C1' O4' UMP sing 371 n n C1' H1' UMP sing 372 n n C2' C3' UMP sing 373 n n C2' H2' UMP sing 374 n n C2' "H2''" UMP sing 375 n n C3' C4' UMP sing 376 n n C3' O3' UMP sing 377 n n C3' H3' UMP sing 378 n n C4' O4' UMP sing 379 n n C4' C5' UMP sing 380 n n C4' H4' UMP sing 381 n n O3' HO3' UMP sing 382 n n C5' O5' UMP sing 383 n n C5' H5' UMP sing 384 n n C5' "H5''" UMP sing 385 n n O5' P UMP sing 386 n n P OP1 UMP doub 387 n n P OP2 UMP sing 388 n n P OP3 UMP sing 389 n n OP2 HOP2 UMP sing 390 n n OP3 HOP3 UMP sing 391 n n # _atom_sites.entry_id 1O25 _atom_sites.fract_transf_matrix[1][1] 0.018288 _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] 0.008569 _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] 0.007056 _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 E 2 UMP A 1 603 603 UMP UMP . F 2 UMP B 1 608 608 UMP UMP . G 2 UMP C 1 613 613 UMP UMP . H 2 UMP D 1 618 618 UMP UMP . I 3 HOH A 1 301 301 HOH HOH . I 3 HOH A 2 304 304 HOH HOH . I 3 HOH A 3 313 313 HOH HOH . I 3 HOH A 4 316 316 HOH HOH . I 3 HOH A 5 321 321 HOH HOH . I 3 HOH A 6 322 322 HOH HOH . I 3 HOH A 7 325 325 HOH HOH . I 3 HOH A 8 327 327 HOH HOH . I 3 HOH A 9 328 328 HOH HOH . I 3 HOH A 10 329 329 HOH HOH . I 3 HOH A 11 332 332 HOH HOH . I 3 HOH A 12 334 334 HOH HOH . I 3 HOH A 13 339 339 HOH HOH . I 3 HOH A 14 340 340 HOH HOH . I 3 HOH A 15 341 341 HOH HOH . I 3 HOH A 16 342 342 HOH HOH . I 3 HOH A 17 350 350 HOH HOH . I 3 HOH A 18 355 355 HOH HOH . I 3 HOH A 19 365 365 HOH HOH . I 3 HOH A 20 368 368 HOH HOH . I 3 HOH A 21 374 374 HOH HOH . I 3 HOH A 22 376 376 HOH HOH . I 3 HOH A 23 377 377 HOH HOH . I 3 HOH A 24 379 379 HOH HOH . I 3 HOH A 25 382 382 HOH HOH . I 3 HOH A 26 383 383 HOH HOH . I 3 HOH A 27 389 389 HOH HOH . I 3 HOH A 28 396 396 HOH HOH . I 3 HOH A 29 397 397 HOH HOH . I 3 HOH A 30 399 399 HOH HOH . I 3 HOH A 31 406 406 HOH HOH . I 3 HOH A 32 409 409 HOH HOH . I 3 HOH A 33 416 416 HOH HOH . I 3 HOH A 34 417 417 HOH HOH . I 3 HOH A 35 423 423 HOH HOH . I 3 HOH A 36 427 427 HOH HOH . I 3 HOH A 37 431 431 HOH HOH . I 3 HOH A 38 435 435 HOH HOH . I 3 HOH A 39 436 436 HOH HOH . I 3 HOH A 40 440 440 HOH HOH . I 3 HOH A 41 441 441 HOH HOH . I 3 HOH A 42 449 449 HOH HOH . I 3 HOH A 43 452 452 HOH HOH . I 3 HOH A 44 454 454 HOH HOH . I 3 HOH A 45 466 466 HOH HOH . I 3 HOH A 46 468 468 HOH HOH . I 3 HOH A 47 479 479 HOH HOH . I 3 HOH A 48 481 481 HOH HOH . I 3 HOH A 49 483 483 HOH HOH . I 3 HOH A 50 492 492 HOH HOH . I 3 HOH A 51 493 493 HOH HOH . I 3 HOH A 52 497 497 HOH HOH . I 3 HOH A 53 503 503 HOH HOH . I 3 HOH A 54 504 504 HOH HOH . I 3 HOH A 55 505 505 HOH HOH . I 3 HOH A 56 514 514 HOH HOH . I 3 HOH A 57 515 515 HOH HOH . J 3 HOH B 1 302 302 HOH HOH . J 3 HOH B 2 308 308 HOH HOH . J 3 HOH B 3 309 309 HOH HOH . J 3 HOH B 4 315 315 HOH HOH . J 3 HOH B 5 338 338 HOH HOH . J 3 HOH B 6 345 345 HOH HOH . J 3 HOH B 7 346 346 HOH HOH . J 3 HOH B 8 347 347 HOH HOH . J 3 HOH B 9 348 348 HOH HOH . J 3 HOH B 10 354 354 HOH HOH . J 3 HOH B 11 356 356 HOH HOH . J 3 HOH B 12 357 357 HOH HOH . J 3 HOH B 13 360 360 HOH HOH . J 3 HOH B 14 361 361 HOH HOH . J 3 HOH B 15 362 362 HOH HOH . J 3 HOH B 16 363 363 HOH HOH . J 3 HOH B 17 369 369 HOH HOH . J 3 HOH B 18 370 370 HOH HOH . J 3 HOH B 19 375 375 HOH HOH . J 3 HOH B 20 378 378 HOH HOH . J 3 HOH B 21 380 380 HOH HOH . J 3 HOH B 22 385 385 HOH HOH . J 3 HOH B 23 386 386 HOH HOH . J 3 HOH B 24 395 395 HOH HOH . J 3 HOH B 25 400 400 HOH HOH . J 3 HOH B 26 401 401 HOH HOH . J 3 HOH B 27 402 402 HOH HOH . J 3 HOH B 28 404 404 HOH HOH . J 3 HOH B 29 413 413 HOH HOH . J 3 HOH B 30 419 419 HOH HOH . J 3 HOH B 31 422 422 HOH HOH . J 3 HOH B 32 438 438 HOH HOH . J 3 HOH B 33 448 448 HOH HOH . J 3 HOH B 34 472 472 HOH HOH . J 3 HOH B 35 475 475 HOH HOH . J 3 HOH B 36 476 476 HOH HOH . J 3 HOH B 37 478 478 HOH HOH . J 3 HOH B 38 482 482 HOH HOH . J 3 HOH B 39 484 484 HOH HOH . J 3 HOH B 40 485 485 HOH HOH . J 3 HOH B 41 486 486 HOH HOH . J 3 HOH B 42 489 489 HOH HOH . J 3 HOH B 43 499 499 HOH HOH . J 3 HOH B 44 508 508 HOH HOH . J 3 HOH B 45 510 510 HOH HOH . J 3 HOH B 46 512 512 HOH HOH . J 3 HOH B 47 519 519 HOH HOH . J 3 HOH B 48 520 520 HOH HOH . J 3 HOH B 49 521 521 HOH HOH . J 3 HOH B 50 524 524 HOH HOH . J 3 HOH B 51 525 525 HOH HOH . K 3 HOH C 1 306 306 HOH HOH . K 3 HOH C 2 311 311 HOH HOH . K 3 HOH C 3 317 317 HOH HOH . K 3 HOH C 4 318 318 HOH HOH . K 3 HOH C 5 319 319 HOH HOH . K 3 HOH C 6 326 326 HOH HOH . K 3 HOH C 7 331 331 HOH HOH . K 3 HOH C 8 335 335 HOH HOH . K 3 HOH C 9 349 349 HOH HOH . K 3 HOH C 10 351 351 HOH HOH . K 3 HOH C 11 352 352 HOH HOH . K 3 HOH C 12 353 353 HOH HOH . K 3 HOH C 13 359 359 HOH HOH . K 3 HOH C 14 364 364 HOH HOH . K 3 HOH C 15 366 366 HOH HOH . K 3 HOH C 16 371 371 HOH HOH . K 3 HOH C 17 372 372 HOH HOH . K 3 HOH C 18 373 373 HOH HOH . K 3 HOH C 19 381 381 HOH HOH . K 3 HOH C 20 388 388 HOH HOH . K 3 HOH C 21 394 394 HOH HOH . K 3 HOH C 22 398 398 HOH HOH . K 3 HOH C 23 407 407 HOH HOH . K 3 HOH C 24 408 408 HOH HOH . K 3 HOH C 25 411 411 HOH HOH . K 3 HOH C 26 412 412 HOH HOH . K 3 HOH C 27 424 424 HOH HOH . K 3 HOH C 28 428 428 HOH HOH . K 3 HOH C 29 432 432 HOH HOH . K 3 HOH C 30 433 433 HOH HOH . K 3 HOH C 31 442 442 HOH HOH . K 3 HOH C 32 444 444 HOH HOH . K 3 HOH C 33 445 445 HOH HOH . K 3 HOH C 34 447 447 HOH HOH . K 3 HOH C 35 451 451 HOH HOH . K 3 HOH C 36 453 453 HOH HOH . K 3 HOH C 37 455 455 HOH HOH . K 3 HOH C 38 456 456 HOH HOH . K 3 HOH C 39 457 457 HOH HOH . K 3 HOH C 40 460 460 HOH HOH . K 3 HOH C 41 461 461 HOH HOH . K 3 HOH C 42 467 467 HOH HOH . K 3 HOH C 43 469 469 HOH HOH . K 3 HOH C 44 470 470 HOH HOH . K 3 HOH C 45 474 474 HOH HOH . K 3 HOH C 46 487 487 HOH HOH . K 3 HOH C 47 488 488 HOH HOH . K 3 HOH C 48 494 494 HOH HOH . K 3 HOH C 49 495 495 HOH HOH . K 3 HOH C 50 500 500 HOH HOH . K 3 HOH C 51 506 506 HOH HOH . K 3 HOH C 52 509 509 HOH HOH . K 3 HOH C 53 511 511 HOH HOH . K 3 HOH C 54 522 522 HOH HOH . L 3 HOH D 1 303 303 HOH HOH . L 3 HOH D 2 305 305 HOH HOH . L 3 HOH D 3 307 307 HOH HOH . L 3 HOH D 4 310 310 HOH HOH . L 3 HOH D 5 312 312 HOH HOH . L 3 HOH D 6 314 314 HOH HOH . L 3 HOH D 7 320 320 HOH HOH . L 3 HOH D 8 323 323 HOH HOH . L 3 HOH D 9 324 324 HOH HOH . L 3 HOH D 10 330 330 HOH HOH . L 3 HOH D 11 333 333 HOH HOH . L 3 HOH D 12 336 336 HOH HOH . L 3 HOH D 13 337 337 HOH HOH . L 3 HOH D 14 343 343 HOH HOH . L 3 HOH D 15 344 344 HOH HOH . L 3 HOH D 16 358 358 HOH HOH . L 3 HOH D 17 367 367 HOH HOH . L 3 HOH D 18 384 384 HOH HOH . L 3 HOH D 19 387 387 HOH HOH . L 3 HOH D 20 390 390 HOH HOH . L 3 HOH D 21 391 391 HOH HOH . L 3 HOH D 22 392 392 HOH HOH . L 3 HOH D 23 393 393 HOH HOH . L 3 HOH D 24 403 403 HOH HOH . L 3 HOH D 25 405 405 HOH HOH . L 3 HOH D 26 410 410 HOH HOH . L 3 HOH D 27 414 414 HOH HOH . L 3 HOH D 28 415 415 HOH HOH . L 3 HOH D 29 418 418 HOH HOH . L 3 HOH D 30 420 420 HOH HOH . L 3 HOH D 31 421 421 HOH HOH . L 3 HOH D 32 425 425 HOH HOH . L 3 HOH D 33 426 426 HOH HOH . L 3 HOH D 34 429 429 HOH HOH . L 3 HOH D 35 430 430 HOH HOH . L 3 HOH D 36 434 434 HOH HOH . L 3 HOH D 37 437 437 HOH HOH . L 3 HOH D 38 439 439 HOH HOH . L 3 HOH D 39 443 443 HOH HOH . L 3 HOH D 40 446 446 HOH HOH . L 3 HOH D 41 450 450 HOH HOH . L 3 HOH D 42 458 458 HOH HOH . L 3 HOH D 43 459 459 HOH HOH . L 3 HOH D 44 462 462 HOH HOH . L 3 HOH D 45 463 463 HOH HOH . L 3 HOH D 46 464 464 HOH HOH . L 3 HOH D 47 465 465 HOH HOH . L 3 HOH D 48 471 471 HOH HOH . L 3 HOH D 49 473 473 HOH HOH . L 3 HOH D 50 477 477 HOH HOH . L 3 HOH D 51 480 480 HOH HOH . L 3 HOH D 52 490 490 HOH HOH . L 3 HOH D 53 491 491 HOH HOH . L 3 HOH D 54 496 496 HOH HOH . L 3 HOH D 55 498 498 HOH HOH . L 3 HOH D 56 501 501 HOH HOH . L 3 HOH D 57 502 502 HOH HOH . L 3 HOH D 58 507 507 HOH HOH . L 3 HOH D 59 513 513 HOH HOH . L 3 HOH D 60 516 516 HOH HOH . L 3 HOH D 61 517 517 HOH HOH . L 3 HOH D 62 518 518 HOH HOH . L 3 HOH D 63 523 523 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 . . . H 2 25.385 49.626 130.594 1 57.27 ? N1 UMP 618 D 1 HETATM 2 C C2 UMP . . . H 2 25.206 50.251 129.28 1 56.83 ? C2 UMP 618 D 1 HETATM 3 N N3 UMP . . . H 2 24.073 51.078 129.193 1 57.81 ? N3 UMP 618 D 1 HETATM 4 C C4 UMP . . . H 2 23.117 51.36 130.208 1 58.01 ? C4 UMP 618 D 1 HETATM 5 C C5 UMP . . . H 2 23.348 50.711 131.473 1 58.42 ? C5 UMP 618 D 1 HETATM 6 C C6 UMP . . . H 2 24.418 49.907 131.618 1 56.88 ? C6 UMP 618 D 1 HETATM 7 O O2 UMP . . . H 2 25.949 50.094 128.317 1 57.98 ? O2 UMP 618 D 1 HETATM 8 O O4 UMP . . . H 2 22.173 52.112 129.971 1 58.67 ? O4 UMP 618 D 1 HETATM 9 C C1' UMP . . . H 2 26.543 48.711 130.846 1 56.52 ? C1' UMP 618 D 1 HETATM 10 C C2' UMP . . . H 2 27.476 49.949 130.983 1 55.74 ? C2' UMP 618 D 1 HETATM 11 C C3' UMP . . . H 2 28.59 49.454 131.992 1 57.21 ? C3' UMP 618 D 1 HETATM 12 C C4' UMP . . . H 2 27.899 48.515 133.007 1 57.83 ? C4' UMP 618 D 1 HETATM 13 O O3' UMP . . . H 2 29.565 48.695 131.247 1 55.26 ? O3' UMP 618 D 1 HETATM 14 O O4' UMP . . . H 2 26.691 48.065 132.211 1 56.75 ? O4' UMP 618 D 1 HETATM 15 C C5' UMP . . . H 2 27.459 49.263 134.29 1 57.68 ? C5' UMP 618 D 1 HETATM 16 O O5' UMP . . . H 2 26.439 50.22 133.909 1 59.17 ? O5' UMP 618 D 1 HETATM 17 P P UMP . . . H 2 25.661 51.236 134.834 1 59.28 ? P UMP 618 D 1 HETATM 18 O OP1 UMP . . . H 2 25.621 52.532 134.109 1 58.75 ? OP1 UMP 618 D 1 HETATM 19 O OP2 UMP . . . H 2 24.29 50.756 135.025 1 59.39 ? OP2 UMP 618 D 1 HETATM 20 O OP3 UMP . . . H 2 26.312 51.432 136.146 1 59.06 ? OP3 UMP 618 D 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #