data_7BES # _model_server_result.job_id U2MLH-4vrEb3QCIpTC-9ig _model_server_result.datetime_utc '2024-10-11 23:22:19' _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":"H","auth_seq_id":302}' # _entry.id 7BES # _exptl.entry_id 7BES _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 484.141 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 ? 3 F N N ? 3 H N N # _chem_comp.formula 'C9 H15 N2 O15 P3' _chem_comp.formula_weight 484.141 _chem_comp.id UTP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE 5'-TRIPHOSPHATE" _chem_comp.type non-polymer _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 PA O1A UTP doub 368 n n PA O2A UTP sing 369 n n PA O3A UTP sing 370 n n PA O5' UTP sing 371 n n O2A H2A UTP sing 372 n n O3A PB UTP sing 373 n n O5' C5' UTP sing 374 n n PB O1B UTP sing 375 n n PB O2B UTP doub 376 n n PB O3B UTP sing 377 n n O1B H1B UTP sing 378 n n O3B PG UTP sing 379 n n PG O1G UTP sing 380 n n PG O2G UTP doub 381 n n PG O3G UTP sing 382 n n O1G H1G UTP sing 383 n n O3G H3G UTP sing 384 n n C5' C4' UTP sing 385 n n C5' "H5'1" UTP sing 386 n n C5' "H5'2" UTP sing 387 n n C4' O4' UTP sing 388 n n C4' C3' UTP sing 389 n n C4' H4' UTP sing 390 n n O4' C1' UTP sing 391 n n C1' C2' UTP sing 392 n n C1' N1 UTP sing 393 n n C1' H1' UTP sing 394 n n C2' O2' UTP sing 395 n n C2' C3' UTP sing 396 n n C2' H2' UTP sing 397 n n O2' HA UTP sing 398 n n C3' O3' UTP sing 399 n n C3' H3' UTP sing 400 n n O3' HB UTP sing 401 n n N1 C6 UTP sing 402 n y N1 C2 UTP sing 403 n y C6 C5 UTP doub 404 n y C6 H6 UTP sing 405 n n C2 O2 UTP doub 406 n n C2 N3 UTP sing 407 n y N3 C4 UTP sing 408 n y N3 H3 UTP sing 409 n n C4 O4 UTP doub 410 n n C4 C5 UTP sing 411 n y C5 H5 UTP sing 412 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 P PA UTP . . . H 3 155.962 133.416 135.529 1 30.64 ? PA UTP 302 C 1 HETATM 2 O O1A UTP . . . H 3 155.519 134.364 134.505 1 30.64 ? O1A UTP 302 C 1 HETATM 3 O O2A UTP . . . H 3 155.772 133.582 137.016 1 30.64 ? O2A UTP 302 C 1 HETATM 4 O O3A UTP . . . H 3 157.461 132.968 135.213 1 30.64 ? O3A UTP 302 C 1 HETATM 5 O O5' UTP . . . H 3 154.955 132.052 135.158 1 30.64 ? O5' UTP 302 C 1 HETATM 6 P PB UTP . . . H 3 157.889 133.122 133.628 1 30.64 ? PB UTP 302 C 1 HETATM 7 O O1B UTP . . . H 3 159.268 132.445 133.687 1 30.64 ? O1B UTP 302 C 1 HETATM 8 O O2B UTP . . . H 3 156.782 132.382 132.916 1 30.64 ? O2B UTP 302 C 1 HETATM 9 O O3B UTP . . . H 3 158.188 134.574 133.231 1 30.64 ? O3B UTP 302 C 1 HETATM 10 P PG UTP . . . H 3 159.631 135.216 133.907 1 30.64 ? PG UTP 302 C 1 HETATM 11 O O1G UTP . . . H 3 159.481 134.887 135.364 1 30.64 ? O1G UTP 302 C 1 HETATM 12 O O2G UTP . . . H 3 160.825 134.67 133.158 1 30.64 ? O2G UTP 302 C 1 HETATM 13 O O3G UTP . . . H 3 159.336 136.709 133.607 1 30.64 ? O3G UTP 302 C 1 HETATM 14 C C5' UTP . . . H 3 155.642 130.966 135.652 1 30.64 ? C5' UTP 302 C 1 HETATM 15 C C4' UTP . . . H 3 154.863 129.73 135.261 1 30.64 ? C4' UTP 302 C 1 HETATM 16 O O4' UTP . . . H 3 153.478 129.994 135.501 1 30.64 ? O4' UTP 302 C 1 HETATM 17 C C1' UTP . . . H 3 152.743 129.577 134.365 1 30.64 ? C1' UTP 302 C 1 HETATM 18 C C2' UTP . . . H 3 153.68 129.874 133.165 1 30.64 ? C2' UTP 302 C 1 HETATM 19 O O2' UTP . . . H 3 153.293 129.038 132.117 1 30.64 ? O2' UTP 302 C 1 HETATM 20 C C3' UTP . . . H 3 155.038 129.498 133.74 1 30.64 ? C3' UTP 302 C 1 HETATM 21 O O3' UTP . . . H 3 155.319 128.146 133.543 1 30.64 ? O3' UTP 302 C 1 HETATM 22 N N1 UTP . . . H 3 151.552 130.386 134.288 1 30.64 ? N1 UTP 302 C 1 HETATM 23 C C6 UTP . . . H 3 151.703 131.768 134.047 1 30.64 ? C6 UTP 302 C 1 HETATM 24 C C2 UTP . . . H 3 150.307 129.793 134.457 1 30.64 ? C2 UTP 302 C 1 HETATM 25 O O2 UTP . . . H 3 150.18 128.569 134.672 1 30.64 ? O2 UTP 302 C 1 HETATM 26 N N3 UTP . . . H 3 149.186 130.601 134.379 1 30.64 ? N3 UTP 302 C 1 HETATM 27 C C4 UTP . . . H 3 149.263 132.008 134.136 1 30.64 ? C4 UTP 302 C 1 HETATM 28 O O4 UTP . . . H 3 148.171 132.623 134.089 1 30.64 ? O4 UTP 302 C 1 HETATM 29 C C5 UTP . . . H 3 150.543 132.547 133.977 1 30.64 ? C5 UTP 302 C 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 29 #