data_6KNL # _model_server_result.job_id NzNjWbJmVuTwwrQtbz56IQ _model_server_result.datetime_utc '2024-12-05 02:19:52' _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 6knl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 6KNL # _exptl.entry_id 6KNL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 244.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URIDINE _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 6KNL _cell.length_a 119.464 _cell.length_b 119.464 _cell.length_c 108.374 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KNL _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,H,I,J,K _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 ? 2 C N N ? 2 E N N # _chem_comp.formula 'C9 H12 N2 O6' _chem_comp.formula_weight 244.201 _chem_comp.id URI _chem_comp.mon_nstd_flag . _chem_comp.name URIDINE _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 N1 C2 URI sing 360 n n N1 C6 URI sing 361 n n N1 C1' URI sing 362 n n C2 N3 URI sing 363 n n C2 O2 URI doub 364 n n N3 C4 URI sing 365 n n N3 H3 URI sing 366 n n C4 C5 URI sing 367 n n C4 O4 URI doub 368 n n C5 C6 URI doub 369 n n C5 H5 URI sing 370 n n C6 H6 URI sing 371 n n C1' C2' URI sing 372 n n C1' O4' URI sing 373 n n C1' H1' URI sing 374 n n C2' C3' URI sing 375 n n C2' O2' URI sing 376 n n C2' H2' URI sing 377 n n C3' C4' URI sing 378 n n C3' O3' URI sing 379 n n C3' H3' URI sing 380 n n C4' O4' URI sing 381 n n C4' C5' URI sing 382 n n C4' H4' URI sing 383 n n O2' HO2' URI sing 384 n n O3' HO3' URI sing 385 n n C5' O5' URI sing 386 n n C5' "H5'1" URI sing 387 n n C5' "H5'2" URI sing 388 n n O5' HO5' URI sing 389 n n # _atom_sites.entry_id 6KNL _atom_sites.fract_transf_matrix[1][1] 0.008371 _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] 0.008371 _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] 0.009227 _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 2 URI A 1 301 2 URI URI . D 3 3PO A 1 302 2 3PO 3PO . E 2 URI B 1 301 1 URI URI . F 3 3PO B 1 302 1 3PO 3PO . G 4 SO4 B 1 303 1 SO4 SO4 . H 4 SO4 B 1 304 2 SO4 SO4 . I 5 EDO B 1 305 1 EDO EDO . J 6 HOH A 1 401 33 HOH HOH . J 6 HOH A 2 402 31 HOH HOH . J 6 HOH A 3 403 5 HOH HOH . J 6 HOH A 4 404 36 HOH HOH . J 6 HOH A 5 405 27 HOH HOH . J 6 HOH A 6 406 7 HOH HOH . J 6 HOH A 7 407 11 HOH HOH . K 6 HOH B 1 401 12 HOH HOH . K 6 HOH B 2 402 18 HOH HOH . K 6 HOH B 3 403 30 HOH HOH . K 6 HOH B 4 404 4 HOH HOH . K 6 HOH B 5 405 26 HOH HOH . K 6 HOH B 6 406 13 HOH HOH . K 6 HOH B 7 407 19 HOH HOH . K 6 HOH B 8 408 23 HOH HOH . K 6 HOH B 9 409 34 HOH HOH . K 6 HOH B 10 410 28 HOH HOH . K 6 HOH B 11 411 10 HOH HOH . K 6 HOH B 12 412 21 HOH HOH . K 6 HOH B 13 413 8 HOH HOH . K 6 HOH B 14 414 24 HOH HOH . K 6 HOH B 15 415 25 HOH HOH . K 6 HOH B 16 416 14 HOH HOH . K 6 HOH B 17 417 2 HOH HOH . K 6 HOH B 18 418 32 HOH HOH . K 6 HOH B 19 419 17 HOH HOH . K 6 HOH B 20 420 6 HOH HOH . K 6 HOH B 21 421 29 HOH HOH . K 6 HOH B 22 422 15 HOH HOH . K 6 HOH B 23 423 16 HOH HOH . K 6 HOH B 24 424 35 HOH HOH . K 6 HOH B 25 425 9 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 N N1 URI . . . C 2 18.387 12.793 -15.73 1 64.18 ? N1 URI 301 A 1 HETATM 2 C C2 URI . . . C 2 18.215 13.02 -17.086 1 72.27 ? C2 URI 301 A 1 HETATM 3 N N3 URI . . . C 2 17.303 13.987 -17.413 1 71.23 ? N3 URI 301 A 1 HETATM 4 C C4 URI . . . C 2 16.546 14.736 -16.542 1 69.89 ? C4 URI 301 A 1 HETATM 5 C C5 URI . . . C 2 16.781 14.45 -15.15 1 67 ? C5 URI 301 A 1 HETATM 6 C C6 URI . . . C 2 17.672 13.507 -14.796 1 63.19 ? C6 URI 301 A 1 HETATM 7 O O2 URI . . . C 2 18.823 12.405 -17.95 1 85.62 ? O2 URI 301 A 1 HETATM 8 O O4 URI . . . C 2 15.757 15.558 -17.012 1 66.37 ? O4 URI 301 A 1 HETATM 9 C C1' URI . . . C 2 19.369 11.754 -15.352 1 64.06 ? C1' URI 301 A 1 HETATM 10 C C2' URI . . . C 2 18.872 10.327 -15.624 1 64.43 ? C2' URI 301 A 1 HETATM 11 C C3' URI . . . C 2 20.206 9.602 -15.86 1 65.03 ? C3' URI 301 A 1 HETATM 12 C C4' URI . . . C 2 21.011 10.652 -16.642 1 65.66 ? C4' URI 301 A 1 HETATM 13 O O2' URI . . . C 2 18.14 9.775 -14.547 1 63.35 ? O2' URI 301 A 1 HETATM 14 O O3' URI . . . C 2 20.909 9.245 -14.674 1 64.79 ? O3' URI 301 A 1 HETATM 15 O O4' URI . . . C 2 20.528 11.936 -16.144 1 61.12 ? O4' URI 301 A 1 HETATM 16 C C5' URI . . . C 2 20.87 10.526 -18.165 1 63.41 ? C5' URI 301 A 1 HETATM 17 O O5' URI . . . C 2 21.209 11.714 -18.869 1 59.46 ? O5' URI 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 17 #