data_1DUD # _model_server_result.job_id AjGRrY_PFQuiL_Q9dnUORA _model_server_result.datetime_utc '2024-11-08 10:30:02' _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 1dud # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":153}' # _entry.id 1DUD # _exptl.entry_id 1DUD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 388.162 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "DEOXYURIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 1DUD _cell.length_a 86.64 _cell.length_b 86.64 _cell.length_c 62.23 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DUD _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 43.32 75.032441 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -43.32 75.032441 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C9 H14 N2 O11 P2' _chem_comp.formula_weight 388.162 _chem_comp.id DUD _chem_comp.mon_nstd_flag . _chem_comp.name "DEOXYURIDINE-5'-DIPHOSPHATE" _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 DUD sing 83 n n N1 C6 DUD sing 84 n n N1 C1' DUD sing 85 n n C2 N3 DUD sing 86 n n C2 O2 DUD doub 87 n n N3 C4 DUD sing 88 n n N3 HN3 DUD sing 89 n n C4 C5 DUD sing 90 n n C4 O4 DUD doub 91 n n C5 C6 DUD doub 92 n n C5 H5 DUD sing 93 n n C6 H6 DUD sing 94 n n C1' C2' DUD sing 95 n n C1' O4' DUD sing 96 n n C1' H1' DUD sing 97 n n C2' C3' DUD sing 98 n n C2' "H2'1" DUD sing 99 n n C2' "H2'2" DUD sing 100 n n C3' C4' DUD sing 101 n n C3' O3' DUD sing 102 n n C3' H3' DUD sing 103 n n C4' O4' DUD sing 104 n n C4' C5' DUD sing 105 n n C4' H4' DUD sing 106 n n O3' HO3' DUD sing 107 n n C5' O5' DUD sing 108 n n C5' "H5'1" DUD sing 109 n n C5' "H5'2" DUD sing 110 n n O5' PA DUD sing 111 n n PA O1A DUD doub 112 n n PA O2A DUD sing 113 n n PA O3A DUD sing 114 n n O2A HOA2 DUD sing 115 n n O3A PB DUD sing 116 n n PB O1B DUD doub 117 n n PB O2B DUD sing 118 n n PB O3B DUD sing 119 n n O2B HOB2 DUD sing 120 n n O3B HOB3 DUD sing 121 n n # _atom_sites.entry_id 1DUD _atom_sites.fract_transf_matrix[1][1] 0.011542 _atom_sites.fract_transf_matrix[1][2] 0.006664 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013328 _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] 0.016069 _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 B 2 DUD A 1 153 150 DUD DUD . C 3 HOH A 1 202 202 HOH HOH . C 3 HOH A 2 203 203 HOH HOH . C 3 HOH A 3 204 204 HOH HOH . C 3 HOH A 4 205 205 HOH HOH . C 3 HOH A 5 207 207 HOH HOH . C 3 HOH A 6 208 208 HOH HOH . C 3 HOH A 7 209 209 HOH HOH . C 3 HOH A 8 210 210 HOH HOH . C 3 HOH A 9 211 211 HOH HOH . C 3 HOH A 10 212 212 HOH HOH . C 3 HOH A 11 213 213 HOH HOH . C 3 HOH A 12 215 215 HOH HOH . C 3 HOH A 13 219 219 HOH HOH . C 3 HOH A 14 220 220 HOH HOH . C 3 HOH A 15 221 221 HOH HOH . C 3 HOH A 16 222 222 HOH HOH . C 3 HOH A 17 223 223 HOH HOH . C 3 HOH A 18 224 224 HOH HOH . C 3 HOH A 19 225 225 HOH HOH . C 3 HOH A 20 226 226 HOH HOH . C 3 HOH A 21 227 227 HOH HOH . C 3 HOH A 22 229 229 HOH HOH . C 3 HOH A 23 230 230 HOH HOH . C 3 HOH A 24 231 231 HOH HOH . C 3 HOH A 25 232 232 HOH HOH . C 3 HOH A 26 233 233 HOH HOH . C 3 HOH A 27 235 235 HOH HOH . C 3 HOH A 28 236 236 HOH HOH . C 3 HOH A 29 237 237 HOH HOH . C 3 HOH A 30 238 238 HOH HOH . C 3 HOH A 31 239 239 HOH HOH . C 3 HOH A 32 240 240 HOH HOH . C 3 HOH A 33 241 241 HOH HOH . C 3 HOH A 34 245 245 HOH HOH . C 3 HOH A 35 246 246 HOH HOH . C 3 HOH A 36 247 247 HOH HOH . C 3 HOH A 37 248 248 HOH HOH . C 3 HOH A 38 250 250 HOH HOH . C 3 HOH A 39 253 253 HOH HOH . C 3 HOH A 40 262 262 HOH HOH . C 3 HOH A 41 263 263 HOH HOH . C 3 HOH A 42 266 266 HOH HOH . C 3 HOH A 43 268 268 HOH HOH . C 3 HOH A 44 270 270 HOH HOH . C 3 HOH A 45 271 271 HOH HOH . C 3 HOH A 46 272 272 HOH HOH . C 3 HOH A 47 273 273 HOH HOH . C 3 HOH A 48 279 279 HOH HOH . C 3 HOH A 49 280 280 HOH HOH . C 3 HOH A 50 281 281 HOH HOH . C 3 HOH A 51 282 282 HOH HOH . C 3 HOH A 52 283 283 HOH HOH . C 3 HOH A 53 287 287 HOH HOH . C 3 HOH A 54 288 288 HOH HOH . C 3 HOH A 55 289 289 HOH HOH . C 3 HOH A 56 290 290 HOH HOH . C 3 HOH A 57 291 291 HOH HOH . C 3 HOH A 58 292 292 HOH HOH . C 3 HOH A 59 293 293 HOH HOH . C 3 HOH A 60 294 294 HOH HOH . C 3 HOH A 61 295 295 HOH HOH . C 3 HOH A 62 296 296 HOH HOH . C 3 HOH A 63 297 297 HOH HOH . C 3 HOH A 64 299 299 HOH HOH . C 3 HOH A 65 306 306 HOH HOH . C 3 HOH A 66 307 307 HOH HOH . C 3 HOH A 67 309 309 HOH HOH . C 3 HOH A 68 311 311 HOH HOH . C 3 HOH A 69 313 313 HOH HOH . C 3 HOH A 70 314 314 HOH HOH . C 3 HOH A 71 317 317 HOH HOH . C 3 HOH A 72 321 321 HOH HOH . C 3 HOH A 73 324 324 HOH HOH . C 3 HOH A 74 326 326 HOH HOH . C 3 HOH A 75 329 329 HOH HOH . C 3 HOH A 76 330 330 HOH HOH . C 3 HOH A 77 331 331 HOH HOH . C 3 HOH A 78 333 333 HOH HOH . C 3 HOH A 79 334 334 HOH HOH . C 3 HOH A 80 339 339 HOH HOH . C 3 HOH A 81 341 341 HOH HOH . C 3 HOH A 82 346 346 HOH HOH . C 3 HOH A 83 348 348 HOH HOH . C 3 HOH A 84 359 359 HOH HOH . C 3 HOH A 85 361 361 HOH HOH . C 3 HOH A 86 365 365 HOH HOH . C 3 HOH A 87 369 369 HOH HOH . C 3 HOH A 88 371 371 HOH HOH . C 3 HOH A 89 373 373 HOH HOH . C 3 HOH A 90 380 380 HOH HOH . C 3 HOH A 91 385 385 HOH HOH . C 3 HOH A 92 390 390 HOH HOH . C 3 HOH A 93 391 391 HOH HOH . C 3 HOH A 94 392 392 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 DUD . . . B 2 -5.345 37.056 33 0.67 18.4 ? N1 DUD 153 A 1 HETATM 2 C C2 DUD . . . B 2 -4.265 36.395 32.454 0.67 17.49 ? C2 DUD 153 A 1 HETATM 3 N N3 DUD . . . B 2 -3.411 37.132 31.702 0.67 17.59 ? N3 DUD 153 A 1 HETATM 4 C C4 DUD . . . B 2 -3.556 38.48 31.405 0.67 18.07 ? C4 DUD 153 A 1 HETATM 5 C C5 DUD . . . B 2 -4.686 39.098 32.009 0.67 17.02 ? C5 DUD 153 A 1 HETATM 6 C C6 DUD . . . B 2 -5.534 38.397 32.783 0.67 16.05 ? C6 DUD 153 A 1 HETATM 7 O O2 DUD . . . B 2 -4.026 35.187 32.625 0.67 16.11 ? O2 DUD 153 A 1 HETATM 8 O O4 DUD . . . B 2 -2.697 39.053 30.745 0.67 19.47 ? O4 DUD 153 A 1 HETATM 9 C C1' DUD . . . B 2 -6.323 36.296 33.862 0.67 22.12 ? C1' DUD 153 A 1 HETATM 10 C C2' DUD . . . B 2 -6.436 36.871 35.262 0.67 25.55 ? C2' DUD 153 A 1 HETATM 11 C C3' DUD . . . B 2 -7.78 37.55 35.338 0.67 27.18 ? C3' DUD 153 A 1 HETATM 12 C C4' DUD . . . B 2 -8.616 36.848 34.266 0.67 29.04 ? C4' DUD 153 A 1 HETATM 13 O O4' DUD . . . B 2 -7.652 36.397 33.27 0.67 26.38 ? O4' DUD 153 A 1 HETATM 14 O O3' DUD . . . B 2 -8.352 37.317 36.609 0.67 28.07 ? O3' DUD 153 A 1 HETATM 15 C C5' DUD . . . B 2 -9.626 37.825 33.648 0.67 36.43 ? C5' DUD 153 A 1 HETATM 16 O O5' DUD . . . B 2 -8.981 39.036 33.133 0.67 48.11 ? O5' DUD 153 A 1 HETATM 17 P PA DUD . . . B 2 -9.654 40.501 32.969 0.67 52.99 ? PA DUD 153 A 1 HETATM 18 O O1A DUD . . . B 2 -10.72 40.615 33.984 0.67 56.55 ? O1A DUD 153 A 1 HETATM 19 O O2A DUD . . . B 2 -8.616 41.583 32.871 0.67 54.33 ? O2A DUD 153 A 1 HETATM 20 O O3A DUD . . . B 2 -10.462 40.534 31.567 0.67 58.86 ? O3A DUD 153 A 1 HETATM 21 P PB DUD . . . B 2 -11.752 39.794 30.9 0.67 62.31 ? PB DUD 153 A 1 HETATM 22 O O1B DUD . . . B 2 -11.491 38.339 30.707 0.67 64.22 ? O1B DUD 153 A 1 HETATM 23 O O2B DUD . . . B 2 -12.048 40.625 29.709 0.67 62.37 ? O2B DUD 153 A 1 HETATM 24 O O3B DUD . . . B 2 -13.012 40.001 31.978 0.67 64.55 ? O3B DUD 153 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #