data_1G8O # _model_server_result.job_id 7MbxCIwqFyzQQt4_G8nvZg _model_server_result.datetime_utc '2024-11-22 09:38:31' _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 1g8o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":474}' # _entry.id 1G8O # _exptl.entry_id 1G8O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-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 1G8O _cell.length_a 95.558 _cell.length_b 95.558 _cell.length_c 112.711 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1G8O _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A OD2 ASP 167 A ASP 225 1_555 B MN MN . A MN 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc2 A OD1 ASP 169 A ASP 227 1_555 B MN MN . A MN 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? metalc ? metalc3 B MN MN . A MN 475 1_555 D O HOH . A HOH 573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-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 N1 C2 U5P sing 358 n n N1 C6 U5P sing 359 n n N1 C1' U5P sing 360 n n C2 N3 U5P sing 361 n n C2 O2 U5P doub 362 n n N3 C4 U5P sing 363 n n N3 HN3 U5P sing 364 n n C4 C5 U5P sing 365 n n C4 O4 U5P doub 366 n n C5 C6 U5P doub 367 n n C5 H5 U5P sing 368 n n C6 H6 U5P sing 369 n n C1' C2' U5P sing 370 n n C1' O4' U5P sing 371 n n C1' H1' U5P sing 372 n n C2' O2' U5P sing 373 n n C2' C3' U5P sing 374 n n C2' H2' U5P sing 375 n n O2' HO2' U5P sing 376 n n C3' C4' U5P sing 377 n n C3' O3' U5P sing 378 n n C3' H3' U5P sing 379 n n C4' O4' U5P sing 380 n n C4' C5' U5P sing 381 n n C4' H4' U5P sing 382 n n O3' HO3' U5P sing 383 n n C5' O5' U5P sing 384 n n C5' "H5'1" U5P sing 385 n n C5' "H5'2" U5P sing 386 n n O5' P U5P sing 387 n n P O1P U5P doub 388 n n P O2P U5P sing 389 n n P O3P U5P sing 390 n n O2P HOP2 U5P sing 391 n n O3P HOP3 U5P sing 392 n n # _atom_sites.entry_id 1G8O _atom_sites.fract_transf_matrix[1][1] 0.010465 _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] 0.010465 _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] 0.008872 _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 MN A 1 475 475 MN MN . C 3 U5P A 1 474 474 U5P U5P . D 4 HOH A 1 476 368 HOH HOH . D 4 HOH A 2 477 369 HOH HOH . D 4 HOH A 3 478 370 HOH HOH . D 4 HOH A 4 479 371 HOH HOH . D 4 HOH A 5 480 372 HOH HOH . D 4 HOH A 6 481 373 HOH HOH . D 4 HOH A 7 482 374 HOH HOH . D 4 HOH A 8 483 375 HOH HOH . D 4 HOH A 9 484 376 HOH HOH . D 4 HOH A 10 485 377 HOH HOH . D 4 HOH A 11 486 378 HOH HOH . D 4 HOH A 12 487 379 HOH HOH . D 4 HOH A 13 488 380 HOH HOH . D 4 HOH A 14 489 381 HOH HOH . D 4 HOH A 15 490 382 HOH HOH . D 4 HOH A 16 491 383 HOH HOH . D 4 HOH A 17 492 385 HOH HOH . D 4 HOH A 18 493 386 HOH HOH . D 4 HOH A 19 494 387 HOH HOH . D 4 HOH A 20 495 388 HOH HOH . D 4 HOH A 21 496 389 HOH HOH . D 4 HOH A 22 497 390 HOH HOH . D 4 HOH A 23 498 391 HOH HOH . D 4 HOH A 24 499 392 HOH HOH . D 4 HOH A 25 500 393 HOH HOH . D 4 HOH A 26 501 394 HOH HOH . D 4 HOH A 27 502 395 HOH HOH . D 4 HOH A 28 503 396 HOH HOH . D 4 HOH A 29 504 397 HOH HOH . D 4 HOH A 30 505 398 HOH HOH . D 4 HOH A 31 506 399 HOH HOH . D 4 HOH A 32 507 400 HOH HOH . D 4 HOH A 33 508 401 HOH HOH . D 4 HOH A 34 509 402 HOH HOH . D 4 HOH A 35 510 403 HOH HOH . D 4 HOH A 36 511 404 HOH HOH . D 4 HOH A 37 512 405 HOH HOH . D 4 HOH A 38 513 406 HOH HOH . D 4 HOH A 39 514 407 HOH HOH . D 4 HOH A 40 515 408 HOH HOH . D 4 HOH A 41 516 409 HOH HOH . D 4 HOH A 42 517 410 HOH HOH . D 4 HOH A 43 518 411 HOH HOH . D 4 HOH A 44 519 412 HOH HOH . D 4 HOH A 45 520 413 HOH HOH . D 4 HOH A 46 521 414 HOH HOH . D 4 HOH A 47 522 415 HOH HOH . D 4 HOH A 48 523 416 HOH HOH . D 4 HOH A 49 524 417 HOH HOH . D 4 HOH A 50 525 418 HOH HOH . D 4 HOH A 51 526 420 HOH HOH . D 4 HOH A 52 527 421 HOH HOH . D 4 HOH A 53 528 423 HOH HOH . D 4 HOH A 54 529 424 HOH HOH . D 4 HOH A 55 530 425 HOH HOH . D 4 HOH A 56 531 426 HOH HOH . D 4 HOH A 57 532 427 HOH HOH . D 4 HOH A 58 533 428 HOH HOH . D 4 HOH A 59 534 429 HOH HOH . D 4 HOH A 60 535 430 HOH HOH . D 4 HOH A 61 536 431 HOH HOH . D 4 HOH A 62 537 432 HOH HOH . D 4 HOH A 63 538 433 HOH HOH . D 4 HOH A 64 539 434 HOH HOH . D 4 HOH A 65 540 435 HOH HOH . D 4 HOH A 66 541 436 HOH HOH . D 4 HOH A 67 542 437 HOH HOH . D 4 HOH A 68 543 438 HOH HOH . D 4 HOH A 69 544 439 HOH HOH . D 4 HOH A 70 545 440 HOH HOH . D 4 HOH A 71 546 441 HOH HOH . D 4 HOH A 72 547 442 HOH HOH . D 4 HOH A 73 548 443 HOH HOH . D 4 HOH A 74 549 444 HOH HOH . D 4 HOH A 75 550 446 HOH HOH . D 4 HOH A 76 551 447 HOH HOH . D 4 HOH A 77 552 448 HOH HOH . D 4 HOH A 78 553 449 HOH HOH . D 4 HOH A 79 554 450 HOH HOH . D 4 HOH A 80 555 451 HOH HOH . D 4 HOH A 81 556 452 HOH HOH . D 4 HOH A 82 557 453 HOH HOH . D 4 HOH A 83 558 454 HOH HOH . D 4 HOH A 84 559 455 HOH HOH . D 4 HOH A 85 560 456 HOH HOH . D 4 HOH A 86 561 457 HOH HOH . D 4 HOH A 87 562 458 HOH HOH . D 4 HOH A 88 563 459 HOH HOH . D 4 HOH A 89 564 460 HOH HOH . D 4 HOH A 90 565 461 HOH HOH . D 4 HOH A 91 566 462 HOH HOH . D 4 HOH A 92 567 463 HOH HOH . D 4 HOH A 93 568 464 HOH HOH . D 4 HOH A 94 569 465 HOH HOH . D 4 HOH A 95 570 467 HOH HOH . D 4 HOH A 96 571 468 HOH HOH . D 4 HOH A 97 572 469 HOH HOH . D 4 HOH A 98 573 470 HOH HOH . D 4 HOH A 99 574 471 HOH HOH . D 4 HOH A 100 575 472 HOH HOH . D 4 HOH A 101 576 473 HOH HOH . D 4 HOH A 102 577 2000 HOH HOH . D 4 HOH A 103 578 2001 HOH HOH . D 4 HOH A 104 579 1000 HOH HOH . D 4 HOH A 105 580 1001 HOH HOH . D 4 HOH A 106 581 1002 HOH HOH . D 4 HOH A 107 582 1003 HOH HOH . D 4 HOH A 108 583 1004 HOH HOH . D 4 HOH A 109 584 1005 HOH HOH . D 4 HOH A 110 585 1006 HOH HOH . D 4 HOH A 111 586 1007 HOH HOH . D 4 HOH A 112 587 1008 HOH HOH . D 4 HOH A 113 588 1009 HOH HOH . D 4 HOH A 114 589 1010 HOH HOH . D 4 HOH A 115 590 1011 HOH HOH . D 4 HOH A 116 591 1012 HOH HOH . D 4 HOH A 117 592 1013 HOH HOH . D 4 HOH A 118 593 1014 HOH HOH . D 4 HOH A 119 594 1015 HOH HOH . D 4 HOH A 120 595 1016 HOH HOH . D 4 HOH A 121 596 1017 HOH HOH . D 4 HOH A 122 597 1018 HOH HOH . D 4 HOH A 123 598 1019 HOH HOH . D 4 HOH A 124 599 1020 HOH HOH . D 4 HOH A 125 600 1021 HOH HOH . D 4 HOH A 126 601 1022 HOH HOH . D 4 HOH A 127 602 1023 HOH HOH . D 4 HOH A 128 603 1024 HOH HOH . D 4 HOH A 129 604 1025 HOH HOH . D 4 HOH A 130 605 1026 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 U5P . . . C 3 84.849 13.99 47.769 0.5 41.21 ? N1 U5P 474 A 1 HETATM 2 C C2 U5P . . . C 3 84.845 12.709 48.328 0.5 39.4 ? C2 U5P 474 A 1 HETATM 3 N N3 U5P . . . C 3 83.638 12.05 48.248 0.5 41.21 ? N3 U5P 474 A 1 HETATM 4 C C4 U5P . . . C 3 82.438 12.516 47.678 0.5 41.03 ? C4 U5P 474 A 1 HETATM 5 C C5 U5P . . . C 3 82.522 13.83 47.135 0.5 40.88 ? C5 U5P 474 A 1 HETATM 6 C C6 U5P . . . C 3 83.656 14.495 47.188 0.5 40.9 ? C6 U5P 474 A 1 HETATM 7 O O2 U5P . . . C 3 85.845 12.25 48.836 0.5 38.47 ? O2 U5P 474 A 1 HETATM 8 O O4 U5P . . . C 3 81.467 11.789 47.697 0.5 42.14 ? O4 U5P 474 A 1 HETATM 9 C C1' U5P . . . C 3 86.123 14.811 47.789 0.5 40.2 ? C1' U5P 474 A 1 HETATM 10 C C2' U5P . . . C 3 87.144 14.249 46.781 0.5 39.29 ? C2' U5P 474 A 1 HETATM 11 O O2' U5P . . . C 3 88.542 14.439 47.185 0.5 36.74 ? O2' U5P 474 A 1 HETATM 12 C C3' U5P . . . C 3 86.736 14.961 45.518 0.5 39.86 ? C3' U5P 474 A 1 HETATM 13 C C4' U5P . . . C 3 86.524 16.372 46.083 0.5 41.75 ? C4' U5P 474 A 1 HETATM 14 O O3' U5P . . . C 3 87.675 14.811 44.412 0.5 39.31 ? O3' U5P 474 A 1 HETATM 15 O O4' U5P . . . C 3 85.831 16.107 47.351 0.5 41 ? O4' U5P 474 A 1 HETATM 16 C C5' U5P . . . C 3 85.549 17.255 45.297 0.5 43.17 ? C5' U5P 474 A 1 HETATM 17 O O5' U5P . . . C 3 85.4 16.789 43.933 0.5 48.36 ? O5' U5P 474 A 1 HETATM 18 P P U5P . . . C 3 83.973 16.411 43.29 0.5 48.74 ? P U5P 474 A 1 HETATM 19 O O1P U5P . . . C 3 83.151 15.338 43.936 0.5 49.03 ? O1P U5P 474 A 1 HETATM 20 O O2P U5P . . . C 3 84.14 15.929 41.89 0.5 51.17 ? O2P U5P 474 A 1 HETATM 21 O O3P U5P . . . C 3 83.28 17.924 43.124 0.5 48.71 ? O3P U5P 474 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #