data_6KNJ # _model_server_result.job_id zt6Ps5nUhxLdSTZzbxJpMg _model_server_result.datetime_utc '2024-10-19 23:59:56' _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":"D","auth_seq_id":302}' # _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 . . . D 4 -18.672 7.699 -8.543 1 101.14 ? PA UTP 302 A 1 HETATM 2 O O1A UTP . . . D 4 -19.342 6.365 -8.591 1 101.14 ? O1A UTP 302 A 1 HETATM 3 O O2A UTP . . . D 4 -19.032 8.639 -7.446 1 101.14 ? O2A UTP 302 A 1 HETATM 4 O O3A UTP . . . D 4 -17.087 7.479 -8.54 1 101.14 ? O3A UTP 302 A 1 HETATM 5 O O5' UTP . . . D 4 -18.852 8.448 -9.939 1 101.14 ? O5' UTP 302 A 1 HETATM 6 P PB UTP . . . D 4 -15.894 7.462 -9.603 1 101.14 ? PB UTP 302 A 1 HETATM 7 O O1B UTP . . . D 4 -15.261 8.806 -9.677 1 101.14 ? O1B UTP 302 A 1 HETATM 8 O O2B UTP . . . D 4 -16.331 6.765 -10.848 1 101.14 ? O2B UTP 302 A 1 HETATM 9 O O3B UTP . . . D 4 -14.882 6.53 -8.807 1 101.14 ? O3B UTP 302 A 1 HETATM 10 P PG UTP . . . D 4 -15.073 5.691 -7.469 1 101.14 ? PG UTP 302 A 1 HETATM 11 O O1G UTP . . . D 4 -13.708 5.199 -7.249 1 101.14 ? O1G UTP 302 A 1 HETATM 12 O O2G UTP . . . D 4 -16.052 4.585 -7.737 1 101.14 ? O2G UTP 302 A 1 HETATM 13 O O3G UTP . . . D 4 -15.518 6.611 -6.394 1 101.14 ? O3G UTP 302 A 1 HETATM 14 C C5' UTP . . . D 4 -20.022 9.277 -10.15 1 101.14 ? C5' UTP 302 A 1 HETATM 15 C C4' UTP . . . D 4 -20.015 9.796 -11.566 1 101.14 ? C4' UTP 302 A 1 HETATM 16 O O4' UTP . . . D 4 -19.511 11.157 -11.561 1 101.14 ? O4' UTP 302 A 1 HETATM 17 C C1' UTP . . . D 4 -18.427 11.293 -12.445 1 101.14 ? C1' UTP 302 A 1 HETATM 18 C C2' UTP . . . D 4 -17.912 9.893 -12.753 1 101.14 ? C2' UTP 302 A 1 HETATM 19 O O2' UTP . . . D 4 -17.406 9.912 -14.068 1 101.14 ? O2' UTP 302 A 1 HETATM 20 C C3' UTP . . . D 4 -19.149 9.005 -12.559 1 101.14 ? C3' UTP 302 A 1 HETATM 21 O O3' UTP . . . D 4 -19.889 8.718 -13.738 1 101.14 ? O3' UTP 302 A 1 HETATM 22 N N1 UTP . . . D 4 -17.387 12.102 -11.797 1 101.14 ? N1 UTP 302 A 1 HETATM 23 C C6 UTP . . . D 4 -17.083 11.958 -10.464 1 101.14 ? C6 UTP 302 A 1 HETATM 24 C C2 UTP . . . D 4 -16.678 12.961 -12.606 1 101.14 ? C2 UTP 302 A 1 HETATM 25 O O2 UTP . . . D 4 -16.92 13.093 -13.797 1 101.14 ? O2 UTP 302 A 1 HETATM 26 N N3 UTP . . . D 4 -15.692 13.666 -11.965 1 101.14 ? N3 UTP 302 A 1 HETATM 27 C C4 UTP . . . D 4 -15.342 13.593 -10.634 1 101.14 ? C4 UTP 302 A 1 HETATM 28 O O4 UTP . . . D 4 -14.431 14.303 -10.217 1 101.14 ? O4 UTP 302 A 1 HETATM 29 C C5 UTP . . . D 4 -16.112 12.663 -9.864 1 101.14 ? C5 UTP 302 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #