data_4FQW # _model_server_result.job_id UR1yxS05Jqfd-CiZg8ozOw _model_server_result.datetime_utc '2024-11-26 12:15:10' _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 4fqw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4FQW # _exptl.entry_id 4FQW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-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 4FQW _cell.length_a 52.3 _cell.length_b 149.22 _cell.length_c 79.36 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4FQW _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 _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_454 -x-1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 -52.3 0 -39.68 # _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 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 UDP sing 412 n n N1 C6 UDP sing 413 n n N1 C1' UDP sing 414 n n C2 N3 UDP sing 415 n n C2 O2 UDP doub 416 n n N3 C4 UDP sing 417 n n N3 HN3 UDP sing 418 n n C4 C5 UDP sing 419 n n C4 O4 UDP doub 420 n n C5 C6 UDP doub 421 n n C5 H5 UDP sing 422 n n C6 H6 UDP sing 423 n n C1' C2' UDP sing 424 n n C1' O4' UDP sing 425 n n C1' H1' UDP sing 426 n n C2' O2' UDP sing 427 n n C2' C3' UDP sing 428 n n C2' H2' UDP sing 429 n n O2' HO2' UDP sing 430 n n C3' C4' UDP sing 431 n n C3' O3' UDP sing 432 n n C3' H3' UDP sing 433 n n C4' O4' UDP sing 434 n n C4' C5' UDP sing 435 n n C4' H4' UDP sing 436 n n O3' HO3' UDP sing 437 n n C5' O5' UDP sing 438 n n C5' "H5'1" UDP sing 439 n n C5' "H5'2" UDP sing 440 n n O5' PA UDP sing 441 n n PA O1A UDP doub 442 n n PA O2A UDP sing 443 n n PA O3A UDP sing 444 n n O2A HOA2 UDP sing 445 n n O3A PB UDP sing 446 n n PB O1B UDP doub 447 n n PB O2B UDP sing 448 n n PB O3B UDP sing 449 n n O2B HOB2 UDP sing 450 n n O3B HOB3 UDP sing 451 n n # _atom_sites.entry_id 4FQW _atom_sites.fract_transf_matrix[1][1] 0.01912 _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] 0.006702 _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] 0.012601 _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 UDP A 1 401 1 UDP UDP . C 3 GAL A 1 402 3 GAL GAL . D 4 PG4 A 1 403 4 PG4 PG4 . E 5 HOH A 1 501 1 HOH HOH . E 5 HOH A 2 502 2 HOH HOH . E 5 HOH A 3 503 3 HOH HOH . E 5 HOH A 4 504 4 HOH HOH . E 5 HOH A 5 505 5 HOH HOH . E 5 HOH A 6 506 6 HOH HOH . E 5 HOH A 7 507 7 HOH HOH . E 5 HOH A 8 508 8 HOH HOH . E 5 HOH A 9 509 9 HOH HOH . E 5 HOH A 10 510 10 HOH HOH . E 5 HOH A 11 511 11 HOH HOH . E 5 HOH A 12 512 12 HOH HOH . E 5 HOH A 13 513 13 HOH HOH . E 5 HOH A 14 514 14 HOH HOH . E 5 HOH A 15 515 15 HOH HOH . E 5 HOH A 16 516 16 HOH HOH . E 5 HOH A 17 517 17 HOH HOH . E 5 HOH A 18 518 18 HOH HOH . E 5 HOH A 19 519 19 HOH HOH . E 5 HOH A 20 520 20 HOH HOH . E 5 HOH A 21 521 21 HOH HOH . E 5 HOH A 22 522 22 HOH HOH . E 5 HOH A 23 523 23 HOH HOH . E 5 HOH A 24 524 24 HOH HOH . E 5 HOH A 25 525 25 HOH HOH . E 5 HOH A 26 526 26 HOH HOH . E 5 HOH A 27 527 27 HOH HOH . E 5 HOH A 28 528 28 HOH HOH . E 5 HOH A 29 529 29 HOH HOH . E 5 HOH A 30 530 30 HOH HOH . E 5 HOH A 31 531 31 HOH HOH . E 5 HOH A 32 532 32 HOH HOH . E 5 HOH A 33 533 33 HOH HOH . E 5 HOH A 34 534 34 HOH HOH . E 5 HOH A 35 535 35 HOH HOH . E 5 HOH A 36 536 36 HOH HOH . E 5 HOH A 37 537 37 HOH HOH . E 5 HOH A 38 538 38 HOH HOH . E 5 HOH A 39 539 39 HOH HOH . E 5 HOH A 40 540 40 HOH HOH . E 5 HOH A 41 541 41 HOH HOH . E 5 HOH A 42 542 42 HOH HOH . E 5 HOH A 43 543 43 HOH HOH . E 5 HOH A 44 544 44 HOH HOH . E 5 HOH A 45 545 45 HOH HOH . E 5 HOH A 46 546 46 HOH HOH . E 5 HOH A 47 547 47 HOH HOH . E 5 HOH A 48 548 48 HOH HOH . E 5 HOH A 49 549 49 HOH HOH . E 5 HOH A 50 550 50 HOH HOH . E 5 HOH A 51 551 51 HOH HOH . E 5 HOH A 52 552 52 HOH HOH . E 5 HOH A 53 553 53 HOH HOH . E 5 HOH A 54 554 54 HOH HOH . E 5 HOH A 55 555 55 HOH HOH . E 5 HOH A 56 556 56 HOH HOH . E 5 HOH A 57 557 57 HOH HOH . E 5 HOH A 58 558 58 HOH HOH . E 5 HOH A 59 559 59 HOH HOH . E 5 HOH A 60 560 60 HOH HOH . E 5 HOH A 61 561 61 HOH HOH . E 5 HOH A 62 562 62 HOH HOH . E 5 HOH A 63 563 63 HOH HOH . E 5 HOH A 64 564 64 HOH HOH . E 5 HOH A 65 565 65 HOH HOH . E 5 HOH A 66 566 66 HOH HOH . E 5 HOH A 67 567 67 HOH HOH . E 5 HOH A 68 568 68 HOH HOH . E 5 HOH A 69 569 69 HOH HOH . E 5 HOH A 70 570 70 HOH HOH . E 5 HOH A 71 571 71 HOH HOH . E 5 HOH A 72 572 72 HOH HOH . E 5 HOH A 73 573 73 HOH HOH . E 5 HOH A 74 574 74 HOH HOH . E 5 HOH A 75 575 75 HOH HOH . E 5 HOH A 76 576 76 HOH HOH . E 5 HOH A 77 577 77 HOH HOH . E 5 HOH A 78 578 78 HOH HOH . E 5 HOH A 79 579 79 HOH HOH . E 5 HOH A 80 580 80 HOH HOH . E 5 HOH A 81 581 81 HOH HOH . E 5 HOH A 82 582 82 HOH HOH . E 5 HOH A 83 583 83 HOH HOH . E 5 HOH A 84 584 84 HOH HOH . E 5 HOH A 85 585 85 HOH HOH . E 5 HOH A 86 586 86 HOH HOH . E 5 HOH A 87 587 87 HOH HOH . E 5 HOH A 88 588 88 HOH HOH . E 5 HOH A 89 589 89 HOH HOH . E 5 HOH A 90 590 90 HOH HOH . E 5 HOH A 91 591 91 HOH HOH . E 5 HOH A 92 592 92 HOH HOH . E 5 HOH A 93 593 93 HOH HOH . E 5 HOH A 94 594 94 HOH HOH . E 5 HOH A 95 595 95 HOH HOH . E 5 HOH A 96 596 96 HOH HOH . E 5 HOH A 97 597 97 HOH HOH . E 5 HOH A 98 598 98 HOH HOH . E 5 HOH A 99 599 99 HOH HOH . E 5 HOH A 100 600 100 HOH HOH . E 5 HOH A 101 601 101 HOH HOH . E 5 HOH A 102 602 102 HOH HOH . E 5 HOH A 103 603 103 HOH HOH . E 5 HOH A 104 604 104 HOH HOH . E 5 HOH A 105 605 105 HOH HOH . E 5 HOH A 106 606 106 HOH HOH . E 5 HOH A 107 607 107 HOH HOH . E 5 HOH A 108 608 108 HOH HOH . E 5 HOH A 109 609 109 HOH HOH . E 5 HOH A 110 610 110 HOH HOH . E 5 HOH A 111 611 111 HOH HOH . E 5 HOH A 112 612 112 HOH HOH . E 5 HOH A 113 613 113 HOH HOH . E 5 HOH A 114 614 114 HOH HOH . E 5 HOH A 115 615 115 HOH HOH . E 5 HOH A 116 616 116 HOH HOH . E 5 HOH A 117 617 117 HOH HOH . E 5 HOH A 118 618 118 HOH HOH . E 5 HOH A 119 619 119 HOH HOH . E 5 HOH A 120 620 120 HOH HOH . E 5 HOH A 121 621 121 HOH HOH . E 5 HOH A 122 622 122 HOH HOH . E 5 HOH A 123 623 123 HOH HOH . E 5 HOH A 124 624 124 HOH HOH . E 5 HOH A 125 625 125 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 UDP . . . B 2 -10.831 21.563 6.028 1 50.62 ? N1 UDP 401 A 1 HETATM 2 C C2 UDP . . . B 2 -9.91 22.13 5.139 1 48.82 ? C2 UDP 401 A 1 HETATM 3 N N3 UDP . . . B 2 -9.106 23.136 5.56 1 42.55 ? N3 UDP 401 A 1 HETATM 4 C C4 UDP . . . B 2 -9.112 23.668 6.884 1 46.24 ? C4 UDP 401 A 1 HETATM 5 C C5 UDP . . . B 2 -9.992 23.119 7.837 1 39.25 ? C5 UDP 401 A 1 HETATM 6 C C6 UDP . . . B 2 -10.832 22.084 7.386 1 52.02 ? C6 UDP 401 A 1 HETATM 7 O O2 UDP . . . B 2 -9.804 21.803 3.963 1 55.09 ? O2 UDP 401 A 1 HETATM 8 O O4 UDP . . . B 2 -8.295 24.584 7.121 1 34.07 ? O4 UDP 401 A 1 HETATM 9 C C1' UDP . . . B 2 -11.716 20.416 5.6 1 55.11 ? C1' UDP 401 A 1 HETATM 10 C C2' UDP . . . B 2 -11.11 18.969 5.976 1 56 ? C2' UDP 401 A 1 HETATM 11 O O2' UDP . . . B 2 -11.337 17.804 5.033 1 48.34 ? O2' UDP 401 A 1 HETATM 12 C C3' UDP . . . B 2 -11.696 18.786 7.384 1 49.13 ? C3' UDP 401 A 1 HETATM 13 C C4' UDP . . . B 2 -13.106 19.324 7.221 1 53.03 ? C4' UDP 401 A 1 HETATM 14 O O4' UDP . . . B 2 -13.002 20.49 6.274 1 51.8 ? O4' UDP 401 A 1 HETATM 15 O O3' UDP . . . B 2 -11.775 17.449 7.679 1 54.32 ? O3' UDP 401 A 1 HETATM 16 C C5' UDP . . . B 2 -13.726 19.531 8.635 1 46.98 ? C5' UDP 401 A 1 HETATM 17 O O5' UDP . . . B 2 -13.667 20.894 9.092 0.2 43.74 ? O5' UDP 401 A 1 HETATM 18 P PA UDP . . . B 2 -13.405 21.151 10.654 0.2 40.45 ? PA UDP 401 A 1 HETATM 19 O O1A UDP . . . B 2 -12.048 20.631 10.963 0.2 39.2 ? O1A UDP 401 A 1 HETATM 20 O O2A UDP . . . B 2 -13.781 22.542 11.005 0.2 36.91 ? O2A UDP 401 A 1 HETATM 21 O O3A UDP . . . B 2 -14.414 20.167 11.348 0.2 35.65 ? O3A UDP 401 A 1 HETATM 22 P PB UDP . . . B 2 -13.749 19.454 12.579 0.2 36.4 ? PB UDP 401 A 1 HETATM 23 O O1B UDP . . . B 2 -12.5 18.645 11.961 0.2 35.37 ? O1B UDP 401 A 1 HETATM 24 O O2B UDP . . . B 2 -13.053 20.583 13.5 0.2 34.63 ? O2B UDP 401 A 1 HETATM 25 O O3B UDP . . . B 2 -14.687 18.596 13.351 0.2 35.19 ? O3B UDP 401 A 1 HETATM 26 H HN3 UDP . . . B 2 -8.473 23.538 4.9 1 44.72 ? HN3 UDP 401 A 1 HETATM 27 H H5 UDP . . . B 2 -9.961 23.35 8.81 1 42.81 ? H5 UDP 401 A 1 HETATM 28 H H6 UDP . . . B 2 -11.25 21.558 8.126 1 51.32 ? H6 UDP 401 A 1 HETATM 29 H H1' UDP . . . B 2 -11.846 20.147 4.65 1 52.32 ? H1' UDP 401 A 1 HETATM 30 H H2' UDP . . . B 2 -10.12 19.097 6.04 1 53.78 ? H2' UDP 401 A 1 HETATM 31 H HO2' UDP . . . B 2 -11.793 18.139 4.297 0 50.26 ? HO2' UDP 401 A 1 HETATM 32 H H3' UDP . . . B 2 -11.261 19.205 8.181 1 50.11 ? H3' UDP 401 A 1 HETATM 33 H H4' UDP . . . B 2 -13.828 19.083 6.572 1 50.94 ? H4' UDP 401 A 1 HETATM 34 H HO3' UDP . . . B 2 -11.378 16.926 6.9 0 56.91 ? HO3' UDP 401 A 1 HETATM 35 H "H5'1" UDP . . . B 2 -14.68 19.271 8.482 1 46.08 ? "H5'1" UDP 401 A 1 HETATM 36 H "H5'2" UDP . . . B 2 -13.336 18.914 9.318 1 45.71 ? "H5'2" UDP 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 697 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 36 #