data_6KNJ # _model_server_result.job_id UsbNOrmApNjedgQG9lok-w _model_server_result.datetime_utc '2025-07-08 06:03:35' _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 6knj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 6KNJ # _exptl.entry_id 6KNJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 4 _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 6KNJ _cell.length_a 117.376 _cell.length_b 117.376 _cell.length_c 110.275 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KNJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 4 D N N ? 4 E 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 347 n n PA O2A UTP sing 348 n n PA O3A UTP sing 349 n n PA O5' UTP sing 350 n n O2A H2A UTP sing 351 n n O3A PB UTP sing 352 n n O5' C5' UTP sing 353 n n PB O1B UTP sing 354 n n PB O2B UTP doub 355 n n PB O3B UTP sing 356 n n O1B H1B UTP sing 357 n n O3B PG UTP sing 358 n n PG O1G UTP sing 359 n n PG O2G UTP doub 360 n n PG O3G UTP sing 361 n n O1G H1G UTP sing 362 n n O3G H3G UTP sing 363 n n C5' C4' UTP sing 364 n n C5' "H5'1" UTP sing 365 n n C5' "H5'2" UTP sing 366 n n C4' O4' UTP sing 367 n n C4' C3' UTP sing 368 n n C4' H4' UTP sing 369 n n O4' C1' UTP sing 370 n n C1' C2' UTP sing 371 n n C1' N1 UTP sing 372 n n C1' H1' UTP sing 373 n n C2' O2' UTP sing 374 n n C2' C3' UTP sing 375 n n C2' H2' UTP sing 376 n n O2' HA UTP sing 377 n n C3' O3' UTP sing 378 n n C3' H3' UTP sing 379 n n O3' HB UTP sing 380 n n N1 C6 UTP sing 381 n y N1 C2 UTP sing 382 n y C6 C5 UTP doub 383 n y C6 H6 UTP sing 384 n n C2 O2 UTP doub 385 n n C2 N3 UTP sing 386 n y N3 C4 UTP sing 387 n y N3 H3 UTP sing 388 n n C4 O4 UTP doub 389 n n C4 C5 UTP sing 390 n y C5 H5 UTP sing 391 n n # _atom_sites.entry_id 6KNJ _atom_sites.fract_transf_matrix[1][1] 0.00852 _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] 0.00852 _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] 0.009068 _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 C 3 SO4 A 1 301 1 SO4 SO4 . D 4 UTP A 1 302 1 UTP UTP . E 4 UTP B 1 301 2 UTP UTP . F 5 GOL B 1 302 1 GOL GOL . G 6 HOH B 1 401 3 HOH HOH . G 6 HOH B 2 402 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 P PA UTP . . . E 4 -11.9 -15.517 -33.028 1 101.14 ? PA UTP 301 B 1 HETATM 2 O O1A UTP . . . E 4 -12.029 -16.282 -34.308 1 101.14 ? O1A UTP 301 B 1 HETATM 3 O O2A UTP . . . E 4 -12.977 -15.656 -31.996 1 101.14 ? O2A UTP 301 B 1 HETATM 4 O O3A UTP . . . E 4 -11.687 -13.958 -33.39 1 101.14 ? O3A UTP 301 B 1 HETATM 5 O O5' UTP . . . E 4 -10.48 -15.858 -32.348 1 101.14 ? O5' UTP 301 B 1 HETATM 6 P PB UTP . . . E 4 -12.604 -12.699 -33.761 1 101.14 ? PB UTP 301 B 1 HETATM 7 O O1B UTP . . . E 4 -12.386 -11.688 -32.687 1 101.14 ? O1B UTP 301 B 1 HETATM 8 O O2B UTP . . . E 4 -12.367 -12.308 -35.184 1 101.14 ? O2B UTP 301 B 1 HETATM 9 O O3B UTP . . . E 4 -14.063 -13.354 -33.646 1 101.14 ? O3B UTP 301 B 1 HETATM 10 P PG UTP . . . E 4 -15.051 -14.08 -34.71 1 101.14 ? PG UTP 301 B 1 HETATM 11 O O1G UTP . . . E 4 -15.559 -15.332 -34.046 1 101.14 ? O1G UTP 301 B 1 HETATM 12 O O2G UTP . . . E 4 -14.257 -14.367 -35.964 1 101.14 ? O2G UTP 301 B 1 HETATM 13 O O3G UTP . . . E 4 -16.146 -13.081 -34.938 1 101.14 ? O3G UTP 301 B 1 HETATM 14 C C5' UTP . . . E 4 -10.157 -14.951 -31.264 1 101.14 ? C5' UTP 301 B 1 HETATM 15 C C4' UTP . . . E 4 -8.678 -14.905 -30.952 1 101.14 ? C4' UTP 301 B 1 HETATM 16 O O4' UTP . . . E 4 -7.876 -15.504 -32.011 1 101.14 ? O4' UTP 301 B 1 HETATM 17 C C1' UTP . . . E 4 -6.879 -14.604 -32.442 1 101.14 ? C1' UTP 301 B 1 HETATM 18 C C2' UTP . . . E 4 -7.37 -13.215 -32.034 1 101.14 ? C2' UTP 301 B 1 HETATM 19 O O2' UTP . . . E 4 -6.29 -12.335 -31.816 1 101.14 ? O2' UTP 301 B 1 HETATM 20 C C3' UTP . . . E 4 -8.151 -13.479 -30.74 1 101.14 ? C3' UTP 301 B 1 HETATM 21 O O3' UTP . . . E 4 -7.446 -13.431 -29.508 1 101.14 ? O3' UTP 301 B 1 HETATM 22 N N1 UTP . . . E 4 -6.729 -14.716 -33.908 1 101.14 ? N1 UTP 301 B 1 HETATM 23 C C6 UTP . . . E 4 -7.452 -15.634 -34.628 1 101.14 ? C6 UTP 301 B 1 HETATM 24 C C2 UTP . . . E 4 -5.882 -13.819 -34.541 1 101.14 ? C2 UTP 301 B 1 HETATM 25 O O2 UTP . . . E 4 -5.217 -12.986 -33.949 1 101.14 ? O2 UTP 301 B 1 HETATM 26 N N3 UTP . . . E 4 -5.82 -13.938 -35.901 1 101.14 ? N3 UTP 301 B 1 HETATM 27 C C4 UTP . . . E 4 -6.506 -14.838 -36.684 1 101.14 ? C4 UTP 301 B 1 HETATM 28 O O4 UTP . . . E 4 -6.344 -14.806 -37.9 1 101.14 ? O4 UTP 301 B 1 HETATM 29 C C5 UTP . . . E 4 -7.367 -15.729 -35.963 1 101.14 ? C5 UTP 301 B 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #