data_3WJY # _model_server_result.job_id a1SXuIWdF7ZDbAbF9uqtKg _model_server_result.datetime_utc '2024-11-26 09:30:14' _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 3wjy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 3WJY # _exptl.entry_id 3WJY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 339.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "6-AMINOURIDINE 5'-MONOPHOSPHATE" _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 3WJY _cell.length_a 58.118 _cell.length_b 103.527 _cell.length_c 74.046 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WJY _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 _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' 4_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 103.527 74.046 # _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 'C9 H14 N3 O9 P' _chem_comp.formula_weight 339.196 _chem_comp.id NUP _chem_comp.mon_nstd_flag . _chem_comp.name "6-AMINOURIDINE 5'-MONOPHOSPHATE" _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 O4 C4 NUP doub 250 n n C4 N2 NUP sing 251 n n C4 C5 NUP sing 252 n n N2 C2 NUP sing 253 n n N2 HN2 NUP sing 254 n n C2 O2 NUP doub 255 n n C2 N1 NUP sing 256 n n C5 C6 NUP doub 257 n n C5 H5 NUP sing 258 n n C6 N1 NUP sing 259 n n C6 N3 NUP sing 260 n n N3 HN31 NUP sing 261 n n N3 HN32 NUP sing 262 n n N1 C1' NUP sing 263 n n C1' C2' NUP sing 264 n n C1' O4' NUP sing 265 n n C1' H1' NUP sing 266 n n O4' C4' NUP sing 267 n n C2' O2' NUP sing 268 n n C2' C3' NUP sing 269 n n C2' H2' NUP sing 270 n n O2' HO2' NUP sing 271 n n C3' O3' NUP sing 272 n n C3' C4' NUP sing 273 n n C3' H3' NUP sing 274 n n O3' HO3' NUP sing 275 n n C4' C5' NUP sing 276 n n C4' H4' NUP sing 277 n n C5' O5' NUP sing 278 n n C5' "H5'1" NUP sing 279 n n C5' "H5'2" NUP sing 280 n n O5' P NUP sing 281 n n P O1P NUP doub 282 n n P O2P NUP sing 283 n n P O3P NUP sing 284 n n O2P HO2P NUP sing 285 n n O3P HO3P NUP sing 286 n n # _atom_sites.entry_id 3WJY _atom_sites.fract_transf_matrix[1][1] 0.017206 _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] 0.009659 _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] 0.013505 _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 NUP A 1 301 301 NUP U6A . C 3 GOL A 1 302 311 GOL GOL . D 4 HOH A 1 401 401 HOH HOH . D 4 HOH A 2 402 402 HOH HOH . D 4 HOH A 3 403 403 HOH HOH . D 4 HOH A 4 404 404 HOH HOH . D 4 HOH A 5 405 405 HOH HOH . D 4 HOH A 6 406 406 HOH HOH . D 4 HOH A 7 407 407 HOH HOH . D 4 HOH A 8 408 408 HOH HOH . D 4 HOH A 9 409 409 HOH HOH . D 4 HOH A 10 410 410 HOH HOH . D 4 HOH A 11 411 411 HOH HOH . D 4 HOH A 12 412 412 HOH HOH . D 4 HOH A 13 413 413 HOH HOH . D 4 HOH A 14 414 414 HOH HOH . D 4 HOH A 15 415 451 HOH HOH . D 4 HOH A 16 416 463 HOH HOH . D 4 HOH A 17 417 477 HOH HOH . D 4 HOH A 18 418 501 HOH HOH . D 4 HOH A 19 419 502 HOH HOH . D 4 HOH A 20 420 503 HOH HOH . D 4 HOH A 21 421 504 HOH HOH . D 4 HOH A 22 422 505 HOH HOH . D 4 HOH A 23 423 506 HOH HOH . D 4 HOH A 24 424 507 HOH HOH . D 4 HOH A 25 425 508 HOH HOH . D 4 HOH A 26 426 509 HOH HOH . D 4 HOH A 27 427 510 HOH HOH . D 4 HOH A 28 428 511 HOH HOH . D 4 HOH A 29 429 512 HOH HOH . D 4 HOH A 30 430 513 HOH HOH . D 4 HOH A 31 431 514 HOH HOH . D 4 HOH A 32 432 515 HOH HOH . D 4 HOH A 33 433 516 HOH HOH . D 4 HOH A 34 434 517 HOH HOH . D 4 HOH A 35 435 518 HOH HOH . D 4 HOH A 36 436 519 HOH HOH . D 4 HOH A 37 437 520 HOH HOH . D 4 HOH A 38 438 521 HOH HOH . D 4 HOH A 39 439 522 HOH HOH . D 4 HOH A 40 440 523 HOH HOH . D 4 HOH A 41 441 524 HOH HOH . D 4 HOH A 42 442 525 HOH HOH . D 4 HOH A 43 443 526 HOH HOH . D 4 HOH A 44 444 527 HOH HOH . D 4 HOH A 45 445 528 HOH HOH . D 4 HOH A 46 446 529 HOH HOH . D 4 HOH A 47 447 530 HOH HOH . D 4 HOH A 48 448 531 HOH HOH . D 4 HOH A 49 449 532 HOH HOH . D 4 HOH A 50 450 533 HOH HOH . D 4 HOH A 51 451 534 HOH HOH . D 4 HOH A 52 452 535 HOH HOH . D 4 HOH A 53 453 536 HOH HOH . D 4 HOH A 54 454 537 HOH HOH . D 4 HOH A 55 455 538 HOH HOH . D 4 HOH A 56 456 539 HOH HOH . D 4 HOH A 57 457 540 HOH HOH . D 4 HOH A 58 458 541 HOH HOH . D 4 HOH A 59 459 542 HOH HOH . D 4 HOH A 60 460 543 HOH HOH . D 4 HOH A 61 461 544 HOH HOH . D 4 HOH A 62 462 545 HOH HOH . D 4 HOH A 63 463 546 HOH HOH . D 4 HOH A 64 464 547 HOH HOH . D 4 HOH A 65 465 548 HOH HOH . D 4 HOH A 66 466 549 HOH HOH . D 4 HOH A 67 467 550 HOH HOH . D 4 HOH A 68 468 551 HOH HOH . D 4 HOH A 69 469 552 HOH HOH . D 4 HOH A 70 470 553 HOH HOH . D 4 HOH A 71 471 554 HOH HOH . D 4 HOH A 72 472 555 HOH HOH . D 4 HOH A 73 473 556 HOH HOH . D 4 HOH A 74 474 557 HOH HOH . D 4 HOH A 75 475 558 HOH HOH . D 4 HOH A 76 476 559 HOH HOH . D 4 HOH A 77 477 560 HOH HOH . D 4 HOH A 78 478 561 HOH HOH . D 4 HOH A 79 479 562 HOH HOH . D 4 HOH A 80 480 563 HOH HOH . D 4 HOH A 81 481 564 HOH HOH . D 4 HOH A 82 482 565 HOH HOH . D 4 HOH A 83 483 566 HOH HOH . D 4 HOH A 84 484 568 HOH HOH . D 4 HOH A 85 485 569 HOH HOH . D 4 HOH A 86 486 570 HOH HOH . D 4 HOH A 87 487 571 HOH HOH . D 4 HOH A 88 488 572 HOH HOH . D 4 HOH A 89 489 573 HOH HOH . D 4 HOH A 90 490 574 HOH HOH . D 4 HOH A 91 491 575 HOH HOH . D 4 HOH A 92 492 576 HOH HOH . D 4 HOH A 93 493 577 HOH HOH . D 4 HOH A 94 494 578 HOH HOH . D 4 HOH A 95 495 579 HOH HOH . D 4 HOH A 96 496 581 HOH HOH . D 4 HOH A 97 497 582 HOH HOH . D 4 HOH A 98 498 583 HOH HOH . D 4 HOH A 99 499 584 HOH HOH . D 4 HOH A 100 500 585 HOH HOH . D 4 HOH A 101 501 586 HOH HOH . D 4 HOH A 102 502 587 HOH HOH . D 4 HOH A 103 503 588 HOH HOH . D 4 HOH A 104 504 589 HOH HOH . D 4 HOH A 105 505 590 HOH HOH . D 4 HOH A 106 506 591 HOH HOH . D 4 HOH A 107 507 592 HOH HOH . D 4 HOH A 108 508 593 HOH HOH . D 4 HOH A 109 509 594 HOH HOH . D 4 HOH A 110 510 595 HOH HOH . D 4 HOH A 111 511 596 HOH HOH . D 4 HOH A 112 512 597 HOH HOH . D 4 HOH A 113 513 599 HOH HOH . D 4 HOH A 114 514 600 HOH HOH . D 4 HOH A 115 515 601 HOH HOH . D 4 HOH A 116 516 602 HOH HOH . D 4 HOH A 117 517 603 HOH HOH . D 4 HOH A 118 518 604 HOH HOH . D 4 HOH A 119 519 605 HOH HOH . D 4 HOH A 120 520 606 HOH HOH . D 4 HOH A 121 521 607 HOH HOH . D 4 HOH A 122 522 608 HOH HOH . D 4 HOH A 123 523 609 HOH HOH . D 4 HOH A 124 524 610 HOH HOH . D 4 HOH A 125 525 611 HOH HOH . D 4 HOH A 126 526 612 HOH HOH . D 4 HOH A 127 527 613 HOH HOH . D 4 HOH A 128 528 614 HOH HOH . D 4 HOH A 129 529 615 HOH HOH . D 4 HOH A 130 530 616 HOH HOH . D 4 HOH A 131 531 617 HOH HOH . D 4 HOH A 132 532 618 HOH HOH . D 4 HOH A 133 533 619 HOH HOH . D 4 HOH A 134 534 620 HOH HOH . D 4 HOH A 135 535 621 HOH HOH . D 4 HOH A 136 536 623 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 O O4 NUP . . . B 2 12.638 41.079 35.765 1 11.96 ? O4 NUP 301 A 1 HETATM 2 C C4 NUP . . . B 2 13.866 40.92 35.91 1 11.92 ? C4 NUP 301 A 1 HETATM 3 N N2 NUP . . . B 2 14.306 39.882 36.658 1 7.96 ? N2 NUP 301 A 1 HETATM 4 C C2 NUP . . . B 2 15.616 39.59 36.687 1 9.71 ? C2 NUP 301 A 1 HETATM 5 O O2 NUP . . . B 2 15.95 38.687 37.444 1 9.55 ? O2 NUP 301 A 1 HETATM 6 C C5 NUP . . . B 2 14.792 41.824 35.385 1 10.33 ? C5 NUP 301 A 1 HETATM 7 C C6 NUP . . . B 2 16.15 41.522 35.502 1 13.05 ? C6 NUP 301 A 1 HETATM 8 N N3 NUP . . . B 2 16.982 42.445 34.876 1 18.05 ? N3 NUP 301 A 1 HETATM 9 N N1 NUP . . . B 2 16.552 40.435 36.219 1 9.01 ? N1 NUP 301 A 1 HETATM 10 C C1' NUP . . . B 2 18.001 40.075 36.269 1 9.68 ? C1' NUP 301 A 1 HETATM 11 O O4' NUP . . . B 2 18.189 38.784 35.711 1 10.29 ? O4' NUP 301 A 1 HETATM 12 C C2' NUP . . . B 2 18.512 39.965 37.692 1 9.03 ? C2' NUP 301 A 1 HETATM 13 O O2' NUP . . . B 2 19.037 41.241 38.075 1 11.73 ? O2' NUP 301 A 1 HETATM 14 C C3' NUP . . . B 2 19.679 38.997 37.504 1 10.71 ? C3' NUP 301 A 1 HETATM 15 O O3' NUP . . . B 2 20.793 39.681 36.871 1 12.79 ? O3' NUP 301 A 1 HETATM 16 C C4' NUP . . . B 2 19.127 38.021 36.504 1 8.14 ? C4' NUP 301 A 1 HETATM 17 C C5' NUP . . . B 2 18.384 36.836 37.141 1 11.08 ? C5' NUP 301 A 1 HETATM 18 O O5' NUP . . . B 2 19.423 36.037 37.721 1 11.05 ? O5' NUP 301 A 1 HETATM 19 P P NUP . . . B 2 19.078 34.742 38.589 1 10.13 ? P NUP 301 A 1 HETATM 20 O O1P NUP . . . B 2 18.959 33.623 37.584 1 10.3 ? O1P NUP 301 A 1 HETATM 21 O O2P NUP . . . B 2 20.248 34.593 39.555 1 11.83 ? O2P NUP 301 A 1 HETATM 22 O O3P NUP . . . B 2 17.798 34.956 39.32 1 10.79 ? O3P NUP 301 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #