data_8UAG # _model_server_result.job_id Idd5K2lZooxHfoOQvP6w8g _model_server_result.datetime_utc '2024-12-18 19:55:06' _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 8uag # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":504}' # _entry.id 8UAG # _exptl.entry_id 8UAG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _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 8UAG _cell.length_a 40.231 _cell.length_b 59.689 _cell.length_c 177.638 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8UAG _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id UPG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # 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 UPG sing 367 n n N1 C6 UPG sing 368 n n N1 C1C UPG sing 369 n n C2 N3 UPG sing 370 n n C2 O2 UPG doub 371 n n N3 C4 UPG sing 372 n n N3 HN3 UPG sing 373 n n C4 C5 UPG sing 374 n n C4 O4 UPG doub 375 n n C5 C6 UPG doub 376 n n C5 H5 UPG sing 377 n n C6 H6 UPG sing 378 n n C1C C2C UPG sing 379 n n C1C O4C UPG sing 380 n n C1C H1C UPG sing 381 n n C2C O2C UPG sing 382 n n C2C C3C UPG sing 383 n n C2C H2C UPG sing 384 n n O2C HO2C UPG sing 385 n n C3C C4C UPG sing 386 n n C3C O3C UPG sing 387 n n C3C H3C UPG sing 388 n n C4C O4C UPG sing 389 n n C4C C5C UPG sing 390 n n C4C H4C UPG sing 391 n n O3C HO3C UPG sing 392 n n C5C O5C UPG sing 393 n n C5C H5C1 UPG sing 394 n n C5C H5C2 UPG sing 395 n n O5C PA UPG sing 396 n n PA O1A UPG doub 397 n n PA O2A UPG sing 398 n n PA O3A UPG sing 399 n n O2A HOA2 UPG sing 400 n n O3A PB UPG sing 401 n n PB O1B UPG doub 402 n n PB O2B UPG sing 403 n n PB O3B UPG sing 404 n n O2B HOB2 UPG sing 405 n n O3B C1' UPG sing 406 n n C1' C2' UPG sing 407 n n C1' O5' UPG sing 408 n n C1' H1' UPG sing 409 n n C2' C3' UPG sing 410 n n C2' O2' UPG sing 411 n n C2' H2' UPG sing 412 n n C3' C4' UPG sing 413 n n C3' O3' UPG sing 414 n n C3' H3' UPG sing 415 n n C4' C5' UPG sing 416 n n C4' O4' UPG sing 417 n n C4' H4' UPG sing 418 n n C5' C6' UPG sing 419 n n C5' O5' UPG sing 420 n n C5' H5' UPG sing 421 n n C6' O6' UPG sing 422 n n C6' "H6'1" UPG sing 423 n n C6' "H6'2" UPG sing 424 n n O2' HO2' UPG sing 425 n n O3' HO3' UPG sing 426 n n O4' HO4' UPG sing 427 n n O6' HO6' UPG sing 428 n n # _atom_sites.entry_id 8UAG _atom_sites.fract_transf_matrix[1][1] 0.024856 _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] 0.016754 _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] 0.005629 _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 MG A 1 501 1 MG MG . C 3 EDO A 1 502 1 EDO EDO . D 3 EDO A 1 503 2 EDO EDO . E 4 UPG A 1 504 501 UPG UPG . F 5 HOH A 1 601 108 HOH HOH . F 5 HOH A 2 602 78 HOH HOH . F 5 HOH A 3 603 99 HOH HOH . F 5 HOH A 4 604 76 HOH HOH . F 5 HOH A 5 605 29 HOH HOH . F 5 HOH A 6 606 72 HOH HOH . F 5 HOH A 7 607 64 HOH HOH . F 5 HOH A 8 608 7 HOH HOH . F 5 HOH A 9 609 105 HOH HOH . F 5 HOH A 10 610 61 HOH HOH . F 5 HOH A 11 611 71 HOH HOH . F 5 HOH A 12 612 113 HOH HOH . F 5 HOH A 13 613 112 HOH HOH . F 5 HOH A 14 614 114 HOH HOH . F 5 HOH A 15 615 3 HOH HOH . F 5 HOH A 16 616 84 HOH HOH . F 5 HOH A 17 617 109 HOH HOH . F 5 HOH A 18 618 15 HOH HOH . F 5 HOH A 19 619 10 HOH HOH . F 5 HOH A 20 620 38 HOH HOH . F 5 HOH A 21 621 16 HOH HOH . F 5 HOH A 22 622 93 HOH HOH . F 5 HOH A 23 623 8 HOH HOH . F 5 HOH A 24 624 80 HOH HOH . F 5 HOH A 25 625 98 HOH HOH . F 5 HOH A 26 626 2 HOH HOH . F 5 HOH A 27 627 4 HOH HOH . F 5 HOH A 28 628 55 HOH HOH . F 5 HOH A 29 629 25 HOH HOH . F 5 HOH A 30 630 36 HOH HOH . F 5 HOH A 31 631 22 HOH HOH . F 5 HOH A 32 632 49 HOH HOH . F 5 HOH A 33 633 28 HOH HOH . F 5 HOH A 34 634 5 HOH HOH . F 5 HOH A 35 635 26 HOH HOH . F 5 HOH A 36 636 101 HOH HOH . F 5 HOH A 37 637 117 HOH HOH . F 5 HOH A 38 638 17 HOH HOH . F 5 HOH A 39 639 20 HOH HOH . F 5 HOH A 40 640 54 HOH HOH . F 5 HOH A 41 641 115 HOH HOH . F 5 HOH A 42 642 56 HOH HOH . F 5 HOH A 43 643 40 HOH HOH . F 5 HOH A 44 644 35 HOH HOH . F 5 HOH A 45 645 45 HOH HOH . F 5 HOH A 46 646 65 HOH HOH . F 5 HOH A 47 647 70 HOH HOH . F 5 HOH A 48 648 95 HOH HOH . F 5 HOH A 49 649 19 HOH HOH . F 5 HOH A 50 650 73 HOH HOH . F 5 HOH A 51 651 111 HOH HOH . F 5 HOH A 52 652 66 HOH HOH . F 5 HOH A 53 653 60 HOH HOH . F 5 HOH A 54 654 1 HOH HOH . F 5 HOH A 55 655 27 HOH HOH . F 5 HOH A 56 656 14 HOH HOH . F 5 HOH A 57 657 30 HOH HOH . F 5 HOH A 58 658 42 HOH HOH . F 5 HOH A 59 659 88 HOH HOH . F 5 HOH A 60 660 48 HOH HOH . F 5 HOH A 61 661 33 HOH HOH . F 5 HOH A 62 662 32 HOH HOH . F 5 HOH A 63 663 69 HOH HOH . F 5 HOH A 64 664 106 HOH HOH . F 5 HOH A 65 665 52 HOH HOH . F 5 HOH A 66 666 12 HOH HOH . F 5 HOH A 67 667 31 HOH HOH . F 5 HOH A 68 668 21 HOH HOH . F 5 HOH A 69 669 63 HOH HOH . F 5 HOH A 70 670 96 HOH HOH . F 5 HOH A 71 671 24 HOH HOH . F 5 HOH A 72 672 34 HOH HOH . F 5 HOH A 73 673 81 HOH HOH . F 5 HOH A 74 674 11 HOH HOH . F 5 HOH A 75 675 92 HOH HOH . F 5 HOH A 76 676 79 HOH HOH . F 5 HOH A 77 677 59 HOH HOH . F 5 HOH A 78 678 97 HOH HOH . F 5 HOH A 79 679 77 HOH HOH . F 5 HOH A 80 680 100 HOH HOH . F 5 HOH A 81 681 13 HOH HOH . F 5 HOH A 82 682 107 HOH HOH . F 5 HOH A 83 683 9 HOH HOH . F 5 HOH A 84 684 68 HOH HOH . F 5 HOH A 85 685 51 HOH HOH . F 5 HOH A 86 686 47 HOH HOH . F 5 HOH A 87 687 94 HOH HOH . F 5 HOH A 88 688 85 HOH HOH . F 5 HOH A 89 689 6 HOH HOH . F 5 HOH A 90 690 37 HOH HOH . F 5 HOH A 91 691 67 HOH HOH . F 5 HOH A 92 692 50 HOH HOH . F 5 HOH A 93 693 53 HOH HOH . F 5 HOH A 94 694 74 HOH HOH . F 5 HOH A 95 695 46 HOH HOH . F 5 HOH A 96 696 44 HOH HOH . F 5 HOH A 97 697 57 HOH HOH . F 5 HOH A 98 698 18 HOH HOH . F 5 HOH A 99 699 110 HOH HOH . F 5 HOH A 100 700 58 HOH HOH . F 5 HOH A 101 701 23 HOH HOH . F 5 HOH A 102 702 39 HOH HOH . F 5 HOH A 103 703 62 HOH HOH . F 5 HOH A 104 704 91 HOH HOH . F 5 HOH A 105 705 87 HOH HOH . F 5 HOH A 106 706 116 HOH HOH . F 5 HOH A 107 707 41 HOH HOH . F 5 HOH A 108 708 102 HOH HOH . F 5 HOH A 109 709 104 HOH HOH . F 5 HOH A 110 710 82 HOH HOH . F 5 HOH A 111 711 75 HOH HOH . F 5 HOH A 112 712 83 HOH HOH . F 5 HOH A 113 713 89 HOH HOH . F 5 HOH A 114 714 43 HOH HOH . F 5 HOH A 115 715 90 HOH HOH . F 5 HOH A 116 716 86 HOH HOH . F 5 HOH A 117 717 103 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 UPG . . . E 4 5.438 5.092 19.955 1 23.32 ? N1 UPG 504 A 1 HETATM 2 C C2 UPG . . . E 4 4.134 4.254 20.051 1 14.7 ? C2 UPG 504 A 1 HETATM 3 N N3 UPG . . . E 4 3.549 3.862 18.694 1 23.23 ? N3 UPG 504 A 1 HETATM 4 C C4 UPG . . . E 4 4.18 4.24 17.431 1 23.98 ? C4 UPG 504 A 1 HETATM 5 C C5 UPG . . . E 4 5.377 5.021 17.422 1 24.31 ? C5 UPG 504 A 1 HETATM 6 C C6 UPG . . . E 4 5.997 5.447 18.663 1 21.25 ? C6 UPG 504 A 1 HETATM 7 O O2 UPG . . . E 4 3.668 3.972 21.096 1 25.51 ? O2 UPG 504 A 1 HETATM 8 O O4 UPG . . . E 4 3.646 3.89 16.392 1 20.38 ? O4 UPG 504 A 1 HETATM 9 C C1C UPG . . . E 4 5.978 5.453 21.11 1 20.5 ? C1C UPG 504 A 1 HETATM 10 C C2C UPG . . . E 4 7.158 4.455 21.485 1 27.76 ? C2C UPG 504 A 1 HETATM 11 O O2C UPG . . . E 4 7.089 4.275 22.942 1 26.52 ? O2C UPG 504 A 1 HETATM 12 C C3C UPG . . . E 4 8.196 5.027 21.066 1 19.87 ? C3C UPG 504 A 1 HETATM 13 C C4C UPG . . . E 4 7.902 6.627 21.439 1 22.29 ? C4C UPG 504 A 1 HETATM 14 O O4C UPG . . . E 4 6.662 6.824 21.046 1 21.81 ? O4C UPG 504 A 1 HETATM 15 O O3C UPG . . . E 4 9.47 4.693 21.725 1 21.42 ? O3C UPG 504 A 1 HETATM 16 C C5C UPG . . . E 4 8.898 7.487 20.767 1 23.17 ? C5C UPG 504 A 1 HETATM 17 O O5C UPG . . . E 4 8.787 7.303 19.395 1 27.57 ? O5C UPG 504 A 1 HETATM 18 P PA UPG . . . E 4 9.449 8.455 18.362 1 18.45 ? PA UPG 504 A 1 HETATM 19 O O1A UPG . . . E 4 8.981 8.147 16.919 1 19.82 ? O1A UPG 504 A 1 HETATM 20 O O2A UPG . . . E 4 10.93 8.507 18.54 1 23.99 ? O2A UPG 504 A 1 HETATM 21 O O3A UPG . . . E 4 8.811 9.916 18.731 1 26.81 ? O3A UPG 504 A 1 HETATM 22 P PB UPG . . . E 4 9.646 11.239 19.157 1 22.97 ? PB UPG 504 A 1 HETATM 23 O O1B UPG . . . E 4 8.587 12.242 19.447 1 19.22 ? O1B UPG 504 A 1 HETATM 24 O O2B UPG . . . E 4 10.577 11.699 18.047 1 22.4 ? O2B UPG 504 A 1 HETATM 25 O O3B UPG . . . E 4 10.54 10.879 20.531 1 22.07 ? O3B UPG 504 A 1 HETATM 26 C C1' UPG . . . E 4 11.201 11.909 21.241 1 17.7 ? C1' UPG 504 A 1 HETATM 27 C C2' UPG . . . E 4 12.681 11.775 20.941 1 22.81 ? C2' UPG 504 A 1 HETATM 28 C C3' UPG . . . E 4 13.192 10.444 21.437 1 26.25 ? C3' UPG 504 A 1 HETATM 29 C C4' UPG . . . E 4 12.947 10.364 22.891 1 27.09 ? C4' UPG 504 A 1 HETATM 30 C C5' UPG . . . E 4 11.466 10.482 23.243 1 24.61 ? C5' UPG 504 A 1 HETATM 31 C C6' UPG . . . E 4 11.246 10.479 24.744 1 31.33 ? C6' UPG 504 A 1 HETATM 32 O O2' UPG . . . E 4 12.855 11.882 19.53 1 22.65 ? O2' UPG 504 A 1 HETATM 33 O O3' UPG . . . E 4 14.598 10.364 21.063 1 27.26 ? O3' UPG 504 A 1 HETATM 34 O O4' UPG . . . E 4 13.442 9.102 23.429 1 24.81 ? O4' UPG 504 A 1 HETATM 35 O O5' UPG . . . E 4 10.867 11.733 22.632 1 19.41 ? O5' UPG 504 A 1 HETATM 36 O O6' UPG . . . E 4 11.637 11.771 25.223 1 35.07 ? O6' UPG 504 A 1 HETATM 37 H HN3 UPG . . . E 4 2.816 3.398 18.673 1 27.87 ? HN3 UPG 504 A 1 HETATM 38 H H5 UPG . . . E 4 5.912 4.995 16.661 1 29.17 ? H5 UPG 504 A 1 HETATM 39 H H6 UPG . . . E 4 6.898 5.676 18.632 1 25.5 ? H6 UPG 504 A 1 HETATM 40 H H1C UPG . . . E 4 5.306 5.471 21.766 1 24.6 ? H1C UPG 504 A 1 HETATM 41 H H2C UPG . . . E 4 7.13 3.619 21.058 1 33.31 ? H2C UPG 504 A 1 HETATM 42 H HO2C UPG . . . E 4 6.831 4.979 23.299 1 31.82 ? HO2C UPG 504 A 1 HETATM 43 H H3C UPG . . . E 4 8.272 4.796 20.16 1 23.85 ? H3C UPG 504 A 1 HETATM 44 H H4C UPG . . . E 4 7.951 6.804 22.36 1 26.75 ? H4C UPG 504 A 1 HETATM 45 H HO3C UPG . . . E 4 9.578 5.179 22.392 1 25.7 ? HO3C UPG 504 A 1 HETATM 46 H H5C1 UPG . . . E 4 8.732 8.387 20.979 1 27.8 ? H5C1 UPG 504 A 1 HETATM 47 H H5C2 UPG . . . E 4 9.762 7.249 21.048 1 27.8 ? H5C2 UPG 504 A 1 HETATM 48 H H1' UPG . . . E 4 10.924 12.766 20.975 1 21.24 ? H1' UPG 504 A 1 HETATM 49 H H2' UPG . . . E 4 13.176 12.461 21.35 1 27.37 ? H2' UPG 504 A 1 HETATM 50 H H3' UPG . . . E 4 12.779 9.698 21.043 1 31.5 ? H3' UPG 504 A 1 HETATM 51 H H4' UPG . . . E 4 13.425 11.065 23.294 1 32.51 ? H4' UPG 504 A 1 HETATM 52 H H5' UPG . . . E 4 11.022 9.724 22.912 1 29.53 ? H5' UPG 504 A 1 HETATM 53 H "H6'1" UPG . . . E 4 11.772 9.814 25.147 1 37.59 ? "H6'1" UPG 504 A 1 HETATM 54 H "H6'2" UPG . . . E 4 10.34 10.325 24.938 1 37.59 ? "H6'2" UPG 504 A 1 HETATM 55 H HO2' UPG . . . E 4 12.752 11.135 19.186 1 27.17 ? HO2' UPG 504 A 1 HETATM 56 H HO3' UPG . . . E 4 14.879 11.126 20.879 1 32.71 ? HO3' UPG 504 A 1 HETATM 57 H HO4' UPG . . . E 4 13.005 8.476 23.107 1 29.78 ? HO4' UPG 504 A 1 HETATM 58 H HO6' UPG . . . E 4 11.56 12.33 24.612 1 42.08 ? HO6' UPG 504 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 58 #