data_5UW0 # _model_server_result.job_id JcZERRiUSTJCeHSLA_djpg _model_server_result.datetime_utc '2024-10-19 13:20:37' _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 5uw0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":801}' # _entry.id 5UW0 # _exptl.entry_id 5UW0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 5UW0 _cell.length_a 193.516 _cell.length_b 204.705 _cell.length_c 206.514 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5UW0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _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,M _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 G N N ? 2 K N 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 448 n n N1 C6 UDP sing 449 n n N1 C1' UDP sing 450 n n C2 N3 UDP sing 451 n n C2 O2 UDP doub 452 n n N3 C4 UDP sing 453 n n N3 HN3 UDP sing 454 n n C4 C5 UDP sing 455 n n C4 O4 UDP doub 456 n n C5 C6 UDP doub 457 n n C5 H5 UDP sing 458 n n C6 H6 UDP sing 459 n n C1' C2' UDP sing 460 n n C1' O4' UDP sing 461 n n C1' H1' UDP sing 462 n n C2' O2' UDP sing 463 n n C2' C3' UDP sing 464 n n C2' H2' UDP sing 465 n n O2' HO2' UDP sing 466 n n C3' C4' UDP sing 467 n n C3' O3' UDP sing 468 n n C3' H3' UDP sing 469 n n C4' O4' UDP sing 470 n n C4' C5' UDP sing 471 n n C4' H4' UDP sing 472 n n O3' HO3' UDP sing 473 n n C5' O5' UDP sing 474 n n C5' "H5'1" UDP sing 475 n n C5' "H5'2" UDP sing 476 n n O5' PA UDP sing 477 n n PA O1A UDP doub 478 n n PA O2A UDP sing 479 n n PA O3A UDP sing 480 n n O2A HOA2 UDP sing 481 n n O3A PB UDP sing 482 n n PB O1B UDP doub 483 n n PB O2B UDP sing 484 n n PB O3B UDP sing 485 n n O2B HOB2 UDP sing 486 n n O3B HOB3 UDP sing 487 n n # _atom_sites.entry_id 5UW0 _atom_sites.fract_transf_matrix[1][1] 0.005168 _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] 0.004885 _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] 0.004842 _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 UDP A 1 801 807 UDP UDP . F 3 G6P A 1 802 808 G6P G6P . G 2 UDP B 1 801 804 UDP UDP . H 3 G6P B 1 802 805 G6P G6P . I 4 U2F C 1 801 803 U2F U2F . J 3 G6P C 1 802 806 G6P G6P . K 2 UDP D 1 801 801 UDP UDP . L 3 G6P D 1 802 802 G6P G6P . M 5 HOH C 1 901 1 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 . . . E 2 67.891 48.449 125.187 1 67.2 ? N1 UDP 801 A 1 HETATM 2 C C2 UDP . . . E 2 67.856 49.439 124.17 1 66.4 ? C2 UDP 801 A 1 HETATM 3 N N3 UDP . . . E 2 67.766 49.092 122.874 1 67.04 ? N3 UDP 801 A 1 HETATM 4 C C4 UDP . . . E 2 67.723 47.802 122.512 1 64.83 ? C4 UDP 801 A 1 HETATM 5 C C5 UDP . . . E 2 67.773 46.792 123.484 1 62.85 ? C5 UDP 801 A 1 HETATM 6 C C6 UDP . . . E 2 67.856 47.144 124.833 1 63.94 ? C6 UDP 801 A 1 HETATM 7 O O2 UDP . . . E 2 67.894 50.655 124.461 1 64.85 ? O2 UDP 801 A 1 HETATM 8 O O4 UDP . . . E 2 67.646 47.53 121.296 1 60.8 ? O4 UDP 801 A 1 HETATM 9 C C1' UDP . . . E 2 67.997 48.902 126.593 1 74.27 ? C1' UDP 801 A 1 HETATM 10 C C2' UDP . . . E 2 67.058 48.231 127.599 1 77.42 ? C2' UDP 801 A 1 HETATM 11 O O2' UDP . . . E 2 65.924 49.08 127.821 1 76.47 ? O2' UDP 801 A 1 HETATM 12 C C3' UDP . . . E 2 67.91 48.037 128.845 1 77.29 ? C3' UDP 801 A 1 HETATM 13 C C4' UDP . . . E 2 69.352 48.144 128.359 1 79.84 ? C4' UDP 801 A 1 HETATM 14 O O4' UDP . . . E 2 69.337 48.693 127.041 1 78.62 ? O4' UDP 801 A 1 HETATM 15 O O3' UDP . . . E 2 67.676 49.055 129.828 1 71.2 ? O3' UDP 801 A 1 HETATM 16 C C5' UDP . . . E 2 70.077 46.806 128.326 1 83.29 ? C5' UDP 801 A 1 HETATM 17 O O5' UDP . . . E 2 70.686 46.63 129.599 1 87.39 ? O5' UDP 801 A 1 HETATM 18 P PA UDP . . . E 2 72.135 45.96 129.774 1 91.09 ? PA UDP 801 A 1 HETATM 19 O O1A UDP . . . E 2 72.153 44.736 128.897 1 87.35 ? O1A UDP 801 A 1 HETATM 20 O O2A UDP . . . E 2 73.191 47.036 129.596 1 83.31 ? O2A UDP 801 A 1 HETATM 21 O O3A UDP . . . E 2 72.08 45.489 131.325 1 96.72 ? O3A UDP 801 A 1 HETATM 22 P PB UDP . . . E 2 70.82 44.707 131.993 1 106.8 ? PB UDP 801 A 1 HETATM 23 O O1B UDP . . . E 2 70.055 44.053 130.863 1 109.17 ? O1B UDP 801 A 1 HETATM 24 O O2B UDP . . . E 2 71.473 43.694 132.901 1 111.73 ? O2B UDP 801 A 1 HETATM 25 O O3B UDP . . . E 2 70.053 45.793 132.715 1 99.41 ? O3B UDP 801 A 1 # _model_server_stats.io_time_ms 148 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 357 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #