data_7BES # _model_server_result.job_id kTvIgb4uBPHWm0NfWjeWlA _model_server_result.datetime_utc '2024-10-11 23:19:45' _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":"D","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 . . . D 2 137.815 124.96 154.661 1 21.86 ? N1 UDP 301 A 1 HETATM 2 C C2 UDP . . . D 2 136.953 124.555 153.616 1 21.86 ? C2 UDP 301 A 1 HETATM 3 N N3 UDP . . . D 2 137.577 124.051 152.466 1 21.86 ? N3 UDP 301 A 1 HETATM 4 C C4 UDP . . . D 2 138.976 123.928 152.297 1 21.86 ? C4 UDP 301 A 1 HETATM 5 C C5 UDP . . . D 2 139.765 124.37 153.426 1 21.86 ? C5 UDP 301 A 1 HETATM 6 C C6 UDP . . . D 2 139.193 124.864 154.554 1 21.86 ? C6 UDP 301 A 1 HETATM 7 O O2 UDP . . . D 2 135.731 124.627 153.679 1 21.86 ? O2 UDP 301 A 1 HETATM 8 O O4 UDP . . . D 2 139.398 123.476 151.253 1 21.86 ? O4 UDP 301 A 1 HETATM 9 C C1' UDP . . . D 2 137.155 125.49 155.864 1 21.86 ? C1' UDP 301 A 1 HETATM 10 C C2' UDP . . . D 2 136.638 124.314 156.742 1 21.86 ? C2' UDP 301 A 1 HETATM 11 O O2' UDP . . . D 2 135.366 123.964 156.305 1 21.86 ? O2' UDP 301 A 1 HETATM 12 C C3' UDP . . . D 2 136.66 124.988 158.139 1 21.86 ? C3' UDP 301 A 1 HETATM 13 C C4' UDP . . . D 2 137.586 126.225 157.957 1 21.86 ? C4' UDP 301 A 1 HETATM 14 O O4' UDP . . . D 2 138.121 126.126 156.647 1 21.86 ? O4' UDP 301 A 1 HETATM 15 O O3' UDP . . . D 2 135.399 125.461 158.48 1 21.86 ? O3' UDP 301 A 1 HETATM 16 C C5' UDP . . . D 2 138.796 126.219 158.969 1 21.86 ? C5' UDP 301 A 1 HETATM 17 O O5' UDP . . . D 2 139.745 125.451 158.439 1 21.86 ? O5' UDP 301 A 1 HETATM 18 P PA UDP . . . D 2 140.519 124.172 159.506 1 21.86 ? PA UDP 301 A 1 HETATM 19 O O1A UDP . . . D 2 141.123 123.338 158.372 1 21.86 ? O1A UDP 301 A 1 HETATM 20 O O2A UDP . . . D 2 139.264 123.683 160.124 1 21.86 ? O2A UDP 301 A 1 HETATM 21 O O3A UDP . . . D 2 141.517 125.064 160.293 1 21.86 ? O3A UDP 301 A 1 HETATM 22 P PB UDP . . . D 2 142.565 124.571 161.608 1 21.86 ? PB UDP 301 A 1 HETATM 23 O O1B UDP . . . D 2 143.715 123.886 160.868 1 21.86 ? O1B UDP 301 A 1 HETATM 24 O O2B UDP . . . D 2 142.938 125.896 162.223 1 21.86 ? O2B UDP 301 A 1 HETATM 25 O O3B UDP . . . D 2 141.698 123.661 162.474 1 21.86 ? O3B UDP 301 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #