data_7BES # _model_server_result.job_id JYOdiUeat4WuOQ4NXRXX9A _model_server_result.datetime_utc '2024-11-21 14:29:10' _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 7bes # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 7BES # _exptl.entry_id 7BES _exptl.method 'ELECTRON MICROSCOPY' # _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 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 7BES _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7BES _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details 'The assembly is composed by 6 chains of UMPK.Those are assembled in 2 trimers symetric with each other. Each trimer bind to 2UTP and 3 UDP ligands.' _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 'point symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 273.52 273.52 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 G 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 328 n n N1 C6 UDP sing 329 n n N1 C1' UDP sing 330 n n C2 N3 UDP sing 331 n n C2 O2 UDP doub 332 n n N3 C4 UDP sing 333 n n N3 HN3 UDP sing 334 n n C4 C5 UDP sing 335 n n C4 O4 UDP doub 336 n n C5 C6 UDP doub 337 n n C5 H5 UDP sing 338 n n C6 H6 UDP sing 339 n n C1' C2' UDP sing 340 n n C1' O4' UDP sing 341 n n C1' H1' UDP sing 342 n n C2' O2' UDP sing 343 n n C2' C3' UDP sing 344 n n C2' H2' UDP sing 345 n n O2' HO2' UDP sing 346 n n C3' C4' UDP sing 347 n n C3' O3' UDP sing 348 n n C3' H3' UDP sing 349 n n C4' O4' UDP sing 350 n n C4' C5' UDP sing 351 n n C4' H4' UDP sing 352 n n O3' HO3' UDP sing 353 n n C5' O5' UDP sing 354 n n C5' "H5'1" UDP sing 355 n n C5' "H5'2" UDP sing 356 n n O5' PA UDP sing 357 n n PA O1A UDP doub 358 n n PA O2A UDP sing 359 n n PA O3A UDP sing 360 n n O2A HOA2 UDP sing 361 n n O3A PB UDP sing 362 n n PB O1B UDP doub 363 n n PB O2B UDP sing 364 n n PB O3B UDP sing 365 n n O2B HOB2 UDP sing 366 n n O3B HOB3 UDP sing 367 n n # _atom_sites.entry_id 7BES _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 D 2 UDP A 1 301 301 UDP UDP . E 2 UDP B 1 301 302 UDP UDP . F 3 UTP B 1 302 401 UTP UTP . G 2 UDP C 1 301 303 UDP UDP . H 3 UTP C 1 302 402 UTP UTP . # 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 2 141.24 114.011 137.737 1 26.35 ? N1 UDP 301 B 1 HETATM 2 C C2 UDP . . . E 2 141.901 114.723 138.765 1 26.35 ? C2 UDP 301 B 1 HETATM 3 N N3 UDP . . . E 2 141.076 115.414 139.662 1 26.35 ? N3 UDP 301 B 1 HETATM 4 C C4 UDP . . . E 2 139.663 115.442 139.6 1 26.35 ? C4 UDP 301 B 1 HETATM 5 C C5 UDP . . . E 2 139.088 114.681 138.51 1 26.35 ? C5 UDP 301 B 1 HETATM 6 C C6 UDP . . . E 2 139.86 113.999 137.624 1 26.35 ? C6 UDP 301 B 1 HETATM 7 O O2 UDP . . . E 2 143.12 114.752 138.893 1 26.35 ? O2 UDP 301 B 1 HETATM 8 O O4 UDP . . . E 2 139.056 116.08 140.436 1 26.35 ? O4 UDP 301 B 1 HETATM 9 C C1' UDP . . . E 2 142.113 113.285 136.8 1 26.35 ? C1' UDP 301 B 1 HETATM 10 C C2' UDP . . . E 2 142.749 112.05 137.517 1 26.35 ? C2' UDP 301 B 1 HETATM 11 O O2' UDP . . . E 2 144.052 111.896 137.06 1 26.35 ? O2' UDP 301 B 1 HETATM 12 C C3' UDP . . . E 2 141.789 110.933 137.061 1 26.35 ? C3' UDP 301 B 1 HETATM 13 C C4' UDP . . . E 2 141.395 111.407 135.646 1 26.35 ? C4' UDP 301 B 1 HETATM 14 O O4' UDP . . . E 2 141.326 112.824 135.723 1 26.35 ? O4' UDP 301 B 1 HETATM 15 O O3' UDP . . . E 2 142.465 109.726 136.922 1 26.35 ? O3' UDP 301 B 1 HETATM 16 C C5' UDP . . . E 2 139.97 110.881 135.218 1 26.35 ? C5' UDP 301 B 1 HETATM 17 O O5' UDP . . . E 2 139.221 110.843 136.318 1 26.35 ? O5' UDP 301 B 1 HETATM 18 P PA UDP . . . E 2 138.648 109.205 136.922 1 26.35 ? PA UDP 301 B 1 HETATM 19 O O1A UDP . . . E 2 139.954 108.513 136.806 1 26.35 ? O1A UDP 301 B 1 HETATM 20 O O2A UDP . . . E 2 138.215 109.672 138.316 1 26.35 ? O2A UDP 301 B 1 HETATM 21 O O3A UDP . . . E 2 137.5 108.947 135.909 1 26.35 ? O3A UDP 301 B 1 HETATM 22 P PB UDP . . . E 2 136.638 107.443 135.651 1 26.35 ? PB UDP 301 B 1 HETATM 23 O O1B UDP . . . E 2 135.708 107.807 134.523 1 26.35 ? O1B UDP 301 B 1 HETATM 24 O O2B UDP . . . E 2 135.934 107.237 136.993 1 26.35 ? O2B UDP 301 B 1 HETATM 25 O O3B UDP . . . E 2 137.725 106.428 135.311 1 26.35 ? O3B UDP 301 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 25 #