data_3KUK # _model_server_result.job_id S-ZXm0wvEmLypZuIBflzag _model_server_result.datetime_utc '2024-12-02 03:57:29' _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 3kuk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":311}' # _entry.id 3KUK # _exptl.entry_id 3KUK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 228.202 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE" _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 3KUK _cell.length_a 82.639 _cell.length_b 82.639 _cell.length_c 259.018 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KUK _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 _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 ? 3 D N N ? 3 F N N # _chem_comp.formula 'C9 H12 N2 O5' _chem_comp.formula_weight 228.202 _chem_comp.id DUR _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE" _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 DUR sing 83 n n N1 C6 DUR sing 84 n n N1 C1' DUR sing 85 n n C2 N3 DUR sing 86 n n C2 O2 DUR doub 87 n n N3 C4 DUR sing 88 n n N3 HN3 DUR sing 89 n n C4 C5 DUR sing 90 n n C4 O4 DUR doub 91 n n C5 C6 DUR doub 92 n n C5 H5 DUR sing 93 n n C6 H6 DUR sing 94 n n C1' C2' DUR sing 95 n n C1' O4' DUR sing 96 n n C1' H1' DUR sing 97 n n C2' C3' DUR sing 98 n n C2' "H2'1" DUR sing 99 n n C2' "H2'2" DUR sing 100 n n C3' C4' DUR sing 101 n n C3' O3' DUR sing 102 n n C3' H3' DUR sing 103 n n C4' O4' DUR sing 104 n n C4' C5' DUR sing 105 n n C4' H4' DUR sing 106 n n O3' HO3' DUR sing 107 n n C5' O5' DUR sing 108 n n C5' "H5'1" DUR sing 109 n n C5' "H5'2" DUR sing 110 n n O5' HO5' DUR sing 111 n n # _atom_sites.entry_id 3KUK _atom_sites.fract_transf_matrix[1][1] 0.012101 _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] 0.012101 _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] 0.003861 _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 SO4 A 1 310 2 SO4 SO4 . D 3 DUR A 1 311 1 DUR DUR . E 2 SO4 B 1 310 1 SO4 SO4 . F 3 DUR B 1 311 1 DUR DUR . G 4 HOH A 1 312 1 HOH HOH . G 4 HOH A 2 313 6 HOH HOH . G 4 HOH A 3 314 7 HOH HOH . G 4 HOH A 4 315 9 HOH HOH . G 4 HOH A 5 316 10 HOH HOH . G 4 HOH A 6 317 11 HOH HOH . G 4 HOH A 7 318 12 HOH HOH . G 4 HOH A 8 319 14 HOH HOH . G 4 HOH A 9 320 15 HOH HOH . G 4 HOH A 10 321 16 HOH HOH . G 4 HOH A 11 322 19 HOH HOH . G 4 HOH A 12 323 21 HOH HOH . G 4 HOH A 13 324 22 HOH HOH . G 4 HOH A 14 325 32 HOH HOH . G 4 HOH A 15 326 33 HOH HOH . G 4 HOH A 16 327 34 HOH HOH . G 4 HOH A 17 328 35 HOH HOH . G 4 HOH A 18 329 41 HOH HOH . G 4 HOH A 19 330 42 HOH HOH . G 4 HOH A 20 331 43 HOH HOH . G 4 HOH A 21 332 44 HOH HOH . G 4 HOH A 22 333 45 HOH HOH . G 4 HOH A 23 334 46 HOH HOH . G 4 HOH A 24 335 48 HOH HOH . G 4 HOH A 25 336 49 HOH HOH . G 4 HOH A 26 337 52 HOH HOH . G 4 HOH A 27 338 53 HOH HOH . G 4 HOH A 28 339 54 HOH HOH . G 4 HOH A 29 340 58 HOH HOH . G 4 HOH A 30 341 59 HOH HOH . G 4 HOH A 31 342 60 HOH HOH . H 4 HOH B 1 312 2 HOH HOH . H 4 HOH B 2 313 3 HOH HOH . H 4 HOH B 3 314 4 HOH HOH . H 4 HOH B 4 315 5 HOH HOH . H 4 HOH B 5 316 8 HOH HOH . H 4 HOH B 6 317 13 HOH HOH . H 4 HOH B 7 318 17 HOH HOH . H 4 HOH B 8 319 18 HOH HOH . H 4 HOH B 9 320 20 HOH HOH . H 4 HOH B 10 321 23 HOH HOH . H 4 HOH B 11 322 24 HOH HOH . H 4 HOH B 12 323 25 HOH HOH . H 4 HOH B 13 324 26 HOH HOH . H 4 HOH B 14 325 27 HOH HOH . H 4 HOH B 15 326 28 HOH HOH . H 4 HOH B 16 327 29 HOH HOH . H 4 HOH B 17 328 30 HOH HOH . H 4 HOH B 18 329 31 HOH HOH . H 4 HOH B 19 330 36 HOH HOH . H 4 HOH B 20 331 37 HOH HOH . H 4 HOH B 21 332 38 HOH HOH . H 4 HOH B 22 333 39 HOH HOH . H 4 HOH B 23 334 40 HOH HOH . H 4 HOH B 24 335 47 HOH HOH . H 4 HOH B 25 336 50 HOH HOH . H 4 HOH B 26 337 51 HOH HOH . H 4 HOH B 27 338 55 HOH HOH . H 4 HOH B 28 339 56 HOH HOH . H 4 HOH B 29 340 57 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 DUR . . . F 3 7.898 42.018 -145.206 1 44.07 ? N1 DUR 311 B 1 HETATM 2 C C2 DUR . . . F 3 8.689 40.842 -144.821 1 40.2 ? C2 DUR 311 B 1 HETATM 3 N N3 DUR . . . F 3 10.045 40.776 -145.135 1 38.62 ? N3 DUR 311 B 1 HETATM 4 C C4 DUR . . . F 3 10.664 41.812 -145.809 1 37.93 ? C4 DUR 311 B 1 HETATM 5 C C5 DUR . . . F 3 9.914 42.944 -146.186 1 39.09 ? C5 DUR 311 B 1 HETATM 6 C C6 DUR . . . F 3 8.51 43.024 -145.872 1 39.28 ? C6 DUR 311 B 1 HETATM 7 O O2 DUR . . . F 3 8.217 39.947 -144.201 1 37.17 ? O2 DUR 311 B 1 HETATM 8 O O4 DUR . . . F 3 12.033 41.701 -146.114 1 34.91 ? O4 DUR 311 B 1 HETATM 9 C C1' DUR . . . F 3 6.44 42.101 -144.949 1 43.2 ? C1' DUR 311 B 1 HETATM 10 C C2' DUR . . . F 3 5.928 41.366 -143.781 1 44.51 ? C2' DUR 311 B 1 HETATM 11 C C3' DUR . . . F 3 5.882 42.332 -142.61 1 47.17 ? C3' DUR 311 B 1 HETATM 12 C C4' DUR . . . F 3 6.092 43.737 -143.342 1 50.1 ? C4' DUR 311 B 1 HETATM 13 O O3' DUR . . . F 3 4.719 42.235 -141.827 1 40.53 ? O3' DUR 311 B 1 HETATM 14 O O4' DUR . . . F 3 5.974 43.42 -144.783 1 52.94 ? O4' DUR 311 B 1 HETATM 15 C C5' DUR . . . F 3 7.257 44.645 -142.946 1 38.29 ? C5' DUR 311 B 1 HETATM 16 O O5' DUR . . . F 3 7.374 45.787 -143.758 1 40.14 ? O5' DUR 311 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 16 #