data_1DBT # _model_server_result.job_id yuNpsKDYonoKjSTyVNyX3A _model_server_result.datetime_utc '2024-11-12 20:40:33' _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 1dbt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":251}' # _entry.id 1DBT # _exptl.entry_id 1DBT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 1DBT _cell.length_a 78.41 _cell.length_b 89.76 _cell.length_c 105.9 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DBT _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,D,E,G,H 1 1 C,F,I 2 1,2 # 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 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 78.41 89.76 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _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 U5P sing 358 n n N1 C6 U5P sing 359 n n N1 C1' U5P sing 360 n n C2 N3 U5P sing 361 n n C2 O2 U5P doub 362 n n N3 C4 U5P sing 363 n n N3 HN3 U5P sing 364 n n C4 C5 U5P sing 365 n n C4 O4 U5P doub 366 n n C5 C6 U5P doub 367 n n C5 H5 U5P sing 368 n n C6 H6 U5P sing 369 n n C1' C2' U5P sing 370 n n C1' O4' U5P sing 371 n n C1' H1' U5P sing 372 n n C2' O2' U5P sing 373 n n C2' C3' U5P sing 374 n n C2' H2' U5P sing 375 n n O2' HO2' U5P sing 376 n n C3' C4' U5P sing 377 n n C3' O3' U5P sing 378 n n C3' H3' U5P sing 379 n n C4' O4' U5P sing 380 n n C4' C5' U5P sing 381 n n C4' H4' U5P sing 382 n n O3' HO3' U5P sing 383 n n C5' O5' U5P sing 384 n n C5' "H5'1" U5P sing 385 n n C5' "H5'2" U5P sing 386 n n O5' P U5P sing 387 n n P O1P U5P doub 388 n n P O2P U5P sing 389 n n P O3P U5P sing 390 n n O2P HOP2 U5P sing 391 n n O3P HOP3 U5P sing 392 n n # _atom_sites.entry_id 1DBT _atom_sites.fract_transf_matrix[1][1] 0.012753 _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] 0.011141 _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] 0.009443 _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 D 2 U5P A 1 250 250 U5P UMP . E 2 U5P B 1 251 250 U5P UMP . F 2 U5P C 1 252 250 U5P UMP . G 3 HOH A 1 251 3 HOH TIP . G 3 HOH A 2 252 4 HOH TIP . G 3 HOH A 3 253 6 HOH TIP . G 3 HOH A 4 254 7 HOH TIP . G 3 HOH A 5 255 9 HOH TIP . G 3 HOH A 6 256 10 HOH TIP . G 3 HOH A 7 257 11 HOH TIP . G 3 HOH A 8 258 13 HOH TIP . G 3 HOH A 9 259 23 HOH TIP . G 3 HOH A 10 260 26 HOH TIP . G 3 HOH A 11 261 27 HOH TIP . G 3 HOH A 12 262 29 HOH TIP . G 3 HOH A 13 263 32 HOH TIP . G 3 HOH A 14 264 35 HOH TIP . G 3 HOH A 15 265 39 HOH TIP . G 3 HOH A 16 266 43 HOH TIP . G 3 HOH A 17 267 50 HOH TIP . G 3 HOH A 18 268 52 HOH TIP . G 3 HOH A 19 269 55 HOH TIP . G 3 HOH A 20 270 67 HOH TIP . G 3 HOH A 21 271 71 HOH TIP . G 3 HOH A 22 272 72 HOH TIP . G 3 HOH A 23 273 75 HOH TIP . G 3 HOH A 24 274 79 HOH TIP . G 3 HOH A 25 275 80 HOH TIP . G 3 HOH A 26 276 84 HOH TIP . G 3 HOH A 27 277 86 HOH TIP . G 3 HOH A 28 278 92 HOH TIP . G 3 HOH A 29 279 94 HOH TIP . G 3 HOH A 30 280 96 HOH TIP . G 3 HOH A 31 281 99 HOH TIP . G 3 HOH A 32 282 102 HOH TIP . G 3 HOH A 33 283 103 HOH TIP . G 3 HOH A 34 284 104 HOH TIP . G 3 HOH A 35 285 105 HOH TIP . G 3 HOH A 36 286 112 HOH TIP . G 3 HOH A 37 287 114 HOH TIP . G 3 HOH A 38 288 117 HOH TIP . G 3 HOH A 39 289 121 HOH TIP . G 3 HOH A 40 290 126 HOH TIP . G 3 HOH A 41 291 133 HOH TIP . G 3 HOH A 42 292 136 HOH TIP . G 3 HOH A 43 293 146 HOH TIP . G 3 HOH A 44 294 151 HOH TIP . G 3 HOH A 45 295 155 HOH TIP . G 3 HOH A 46 296 157 HOH TIP . G 3 HOH A 47 297 164 HOH TIP . G 3 HOH A 48 298 167 HOH TIP . G 3 HOH A 49 299 170 HOH TIP . G 3 HOH A 50 300 171 HOH TIP . G 3 HOH A 51 301 172 HOH TIP . G 3 HOH A 52 302 181 HOH TIP . G 3 HOH A 53 303 182 HOH TIP . G 3 HOH A 54 304 183 HOH TIP . G 3 HOH A 55 305 186 HOH TIP . G 3 HOH A 56 306 187 HOH TIP . G 3 HOH A 57 307 189 HOH TIP . G 3 HOH A 58 308 192 HOH TIP . G 3 HOH A 59 309 197 HOH TIP . G 3 HOH A 60 310 203 HOH TIP . G 3 HOH A 61 311 204 HOH TIP . G 3 HOH A 62 312 209 HOH TIP . G 3 HOH A 63 313 212 HOH TIP . G 3 HOH A 64 314 218 HOH TIP . G 3 HOH A 65 315 221 HOH TIP . H 3 HOH B 1 252 1 HOH TIP . H 3 HOH B 2 253 12 HOH TIP . H 3 HOH B 3 254 20 HOH TIP . H 3 HOH B 4 255 22 HOH TIP . H 3 HOH B 5 256 30 HOH TIP . H 3 HOH B 6 257 31 HOH TIP . H 3 HOH B 7 258 37 HOH TIP . H 3 HOH B 8 259 38 HOH TIP . H 3 HOH B 9 260 41 HOH TIP . H 3 HOH B 10 261 44 HOH TIP . H 3 HOH B 11 262 47 HOH TIP . H 3 HOH B 12 263 51 HOH TIP . H 3 HOH B 13 264 54 HOH TIP . H 3 HOH B 14 265 56 HOH TIP . H 3 HOH B 15 266 57 HOH TIP . H 3 HOH B 16 267 59 HOH TIP . H 3 HOH B 17 268 60 HOH TIP . H 3 HOH B 18 269 61 HOH TIP . H 3 HOH B 19 270 63 HOH TIP . H 3 HOH B 20 271 64 HOH TIP . H 3 HOH B 21 272 73 HOH TIP . H 3 HOH B 22 273 76 HOH TIP . H 3 HOH B 23 274 82 HOH TIP . H 3 HOH B 24 275 85 HOH TIP . H 3 HOH B 25 276 90 HOH TIP . H 3 HOH B 26 277 95 HOH TIP . H 3 HOH B 27 278 100 HOH TIP . H 3 HOH B 28 279 107 HOH TIP . H 3 HOH B 29 280 109 HOH TIP . H 3 HOH B 30 281 110 HOH TIP . H 3 HOH B 31 282 111 HOH TIP . H 3 HOH B 32 283 115 HOH TIP . H 3 HOH B 33 284 119 HOH TIP . H 3 HOH B 34 285 122 HOH TIP . H 3 HOH B 35 286 124 HOH TIP . H 3 HOH B 36 287 128 HOH TIP . H 3 HOH B 37 288 129 HOH TIP . H 3 HOH B 38 289 132 HOH TIP . H 3 HOH B 39 290 137 HOH TIP . H 3 HOH B 40 291 138 HOH TIP . H 3 HOH B 41 292 140 HOH TIP . H 3 HOH B 42 293 142 HOH TIP . H 3 HOH B 43 294 147 HOH TIP . H 3 HOH B 44 295 149 HOH TIP . H 3 HOH B 45 296 150 HOH TIP . H 3 HOH B 46 297 165 HOH TIP . H 3 HOH B 47 298 168 HOH TIP . H 3 HOH B 48 299 169 HOH TIP . H 3 HOH B 49 300 173 HOH TIP . H 3 HOH B 50 301 174 HOH TIP . H 3 HOH B 51 302 179 HOH TIP . H 3 HOH B 52 303 184 HOH TIP . H 3 HOH B 53 304 185 HOH TIP . H 3 HOH B 54 305 190 HOH TIP . H 3 HOH B 55 306 193 HOH TIP . H 3 HOH B 56 307 194 HOH TIP . H 3 HOH B 57 308 195 HOH TIP . H 3 HOH B 58 309 198 HOH TIP . H 3 HOH B 59 310 199 HOH TIP . H 3 HOH B 60 311 201 HOH TIP . H 3 HOH B 61 312 205 HOH TIP . H 3 HOH B 62 313 206 HOH TIP . H 3 HOH B 63 314 210 HOH TIP . H 3 HOH B 64 315 213 HOH TIP . H 3 HOH B 65 316 214 HOH TIP . H 3 HOH B 66 317 215 HOH TIP . H 3 HOH B 67 318 217 HOH TIP . H 3 HOH B 68 319 222 HOH TIP . H 3 HOH B 69 320 223 HOH TIP . H 3 HOH B 70 321 224 HOH TIP . H 3 HOH B 71 322 225 HOH TIP . H 3 HOH B 72 323 226 HOH TIP . I 3 HOH C 1 253 2 HOH TIP . I 3 HOH C 2 254 5 HOH TIP . I 3 HOH C 3 255 8 HOH TIP . I 3 HOH C 4 256 14 HOH TIP . I 3 HOH C 5 257 15 HOH TIP . I 3 HOH C 6 258 16 HOH TIP . I 3 HOH C 7 259 17 HOH TIP . I 3 HOH C 8 260 18 HOH TIP . I 3 HOH C 9 261 19 HOH TIP . I 3 HOH C 10 262 21 HOH TIP . I 3 HOH C 11 263 24 HOH TIP . I 3 HOH C 12 264 25 HOH TIP . I 3 HOH C 13 265 28 HOH TIP . I 3 HOH C 14 266 33 HOH TIP . I 3 HOH C 15 267 34 HOH TIP . I 3 HOH C 16 268 36 HOH TIP . I 3 HOH C 17 269 40 HOH TIP . I 3 HOH C 18 270 42 HOH TIP . I 3 HOH C 19 271 45 HOH TIP . I 3 HOH C 20 272 46 HOH TIP . I 3 HOH C 21 273 48 HOH TIP . I 3 HOH C 22 274 49 HOH TIP . I 3 HOH C 23 275 53 HOH TIP . I 3 HOH C 24 276 58 HOH TIP . I 3 HOH C 25 277 62 HOH TIP . I 3 HOH C 26 278 65 HOH TIP . I 3 HOH C 27 279 66 HOH TIP . I 3 HOH C 28 280 68 HOH TIP . I 3 HOH C 29 281 69 HOH TIP . I 3 HOH C 30 282 70 HOH TIP . I 3 HOH C 31 283 74 HOH TIP . I 3 HOH C 32 284 77 HOH TIP . I 3 HOH C 33 285 78 HOH TIP . I 3 HOH C 34 286 81 HOH TIP . I 3 HOH C 35 287 83 HOH TIP . I 3 HOH C 36 288 87 HOH TIP . I 3 HOH C 37 289 88 HOH TIP . I 3 HOH C 38 290 89 HOH TIP . I 3 HOH C 39 291 91 HOH TIP . I 3 HOH C 40 292 93 HOH TIP . I 3 HOH C 41 293 97 HOH TIP . I 3 HOH C 42 294 98 HOH TIP . I 3 HOH C 43 295 101 HOH TIP . I 3 HOH C 44 296 106 HOH TIP . I 3 HOH C 45 297 108 HOH TIP . I 3 HOH C 46 298 113 HOH TIP . I 3 HOH C 47 299 116 HOH TIP . I 3 HOH C 48 300 118 HOH TIP . I 3 HOH C 49 301 120 HOH TIP . I 3 HOH C 50 302 123 HOH TIP . I 3 HOH C 51 303 125 HOH TIP . I 3 HOH C 52 304 127 HOH TIP . I 3 HOH C 53 305 130 HOH TIP . I 3 HOH C 54 306 131 HOH TIP . I 3 HOH C 55 307 134 HOH TIP . I 3 HOH C 56 308 135 HOH TIP . I 3 HOH C 57 309 139 HOH TIP . I 3 HOH C 58 310 141 HOH TIP . I 3 HOH C 59 311 143 HOH TIP . I 3 HOH C 60 312 144 HOH TIP . I 3 HOH C 61 313 145 HOH TIP . I 3 HOH C 62 314 148 HOH TIP . I 3 HOH C 63 315 152 HOH TIP . I 3 HOH C 64 316 153 HOH TIP . I 3 HOH C 65 317 154 HOH TIP . I 3 HOH C 66 318 156 HOH TIP . I 3 HOH C 67 319 158 HOH TIP . I 3 HOH C 68 320 159 HOH TIP . I 3 HOH C 69 321 160 HOH TIP . I 3 HOH C 70 322 161 HOH TIP . I 3 HOH C 71 323 162 HOH TIP . I 3 HOH C 72 324 163 HOH TIP . I 3 HOH C 73 325 166 HOH TIP . I 3 HOH C 74 326 175 HOH TIP . I 3 HOH C 75 327 176 HOH TIP . I 3 HOH C 76 328 177 HOH TIP . I 3 HOH C 77 329 178 HOH TIP . I 3 HOH C 78 330 180 HOH TIP . I 3 HOH C 79 331 188 HOH TIP . I 3 HOH C 80 332 191 HOH TIP . I 3 HOH C 81 333 196 HOH TIP . I 3 HOH C 82 334 200 HOH TIP . I 3 HOH C 83 335 202 HOH TIP . I 3 HOH C 84 336 207 HOH TIP . I 3 HOH C 85 337 208 HOH TIP . I 3 HOH C 86 338 211 HOH TIP . I 3 HOH C 87 339 216 HOH TIP . I 3 HOH C 88 340 219 HOH TIP . I 3 HOH C 89 341 220 HOH TIP . # 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 U5P . . . E 2 54.499 65.713 6.728 1 22.36 ? N1 U5P 251 B 1 HETATM 2 C C2 U5P . . . E 2 53.636 64.872 6.002 1 22.93 ? C2 U5P 251 B 1 HETATM 3 N N3 U5P . . . E 2 52.472 64.529 6.668 1 21.63 ? N3 U5P 251 B 1 HETATM 4 C C4 U5P . . . E 2 52.088 64.926 7.955 1 20.81 ? C4 U5P 251 B 1 HETATM 5 C C5 U5P . . . E 2 53.019 65.771 8.613 1 20.97 ? C5 U5P 251 B 1 HETATM 6 C C6 U5P . . . E 2 54.144 66.126 8.015 1 22.8 ? C6 U5P 251 B 1 HETATM 7 O O2 U5P . . . E 2 53.916 64.494 4.872 1 25.95 ? O2 U5P 251 B 1 HETATM 8 O O4 U5P . . . E 2 51.036 64.533 8.387 1 21.92 ? O4 U5P 251 B 1 HETATM 9 C C1' U5P . . . E 2 55.786 66.177 6.16 1 21.71 ? C1' U5P 251 B 1 HETATM 10 C C2' U5P . . . E 2 56.806 65.124 5.743 1 21.4 ? C2' U5P 251 B 1 HETATM 11 O O2' U5P . . . E 2 57.716 64.766 6.792 1 22.93 ? O2' U5P 251 B 1 HETATM 12 C C3' U5P . . . E 2 57.502 65.692 4.499 1 20.97 ? C3' U5P 251 B 1 HETATM 13 C C4' U5P . . . E 2 56.49 66.705 3.976 1 21.59 ? C4' U5P 251 B 1 HETATM 14 O O3' U5P . . . E 2 58.825 66.214 4.794 1 18.83 ? O3' U5P 251 B 1 HETATM 15 O O4' U5P . . . E 2 55.608 67.051 5.073 1 21.31 ? O4' U5P 251 B 1 HETATM 16 C C5' U5P . . . E 2 55.595 66.273 2.825 1 21.51 ? C5' U5P 251 B 1 HETATM 17 O O5' U5P . . . E 2 56.348 65.527 1.852 1 25.13 ? O5' U5P 251 B 1 HETATM 18 P P U5P . . . E 2 55.854 65.307 0.343 1 23.85 ? P U5P 251 B 1 HETATM 19 O O1P U5P . . . E 2 56.915 65.12 -0.694 1 25.42 ? O1P U5P 251 B 1 HETATM 20 O O2P U5P . . . E 2 55.074 66.475 -0.138 1 22.79 ? O2P U5P 251 B 1 HETATM 21 O O3P U5P . . . E 2 54.788 64.06 0.522 1 25.18 ? O3P U5P 251 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #