data_5KM4 # _model_server_result.job_id MHCxgHPhOyiCejaBGNzreg _model_server_result.datetime_utc '2024-11-26 13:25:18' _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 5km4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 5KM4 # _exptl.entry_id 5KM4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 450.078 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5-IODOURIDINE-5'-MONOPHOSPHATE" _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 93.98 _cell.angle_gamma 90 _cell.entry_id 5KM4 _cell.length_a 78.852 _cell.length_b 46.309 _cell.length_c 63.817 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KM4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C9 H12 I N2 O9 P' _chem_comp.formula_weight 450.078 _chem_comp.id IU _chem_comp.mon_nstd_flag n _chem_comp.name "5-IODOURIDINE-5'-MONOPHOSPHATE" _chem_comp.type 'rna linking' _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 P OP1 IU doub 173 n n P OP2 IU sing 174 n n P OP3 IU sing 175 n n P O5' IU sing 176 n n OP2 HOP2 IU sing 177 n n OP3 HOP3 IU sing 178 n n O5' C5' IU sing 179 n n C5' C4' IU sing 180 n n C5' H5' IU sing 181 n n C5' "H5''" IU sing 182 n n C4' O4' IU sing 183 n n C4' C3' IU sing 184 n n C4' H4' IU sing 185 n n O4' C1' IU sing 186 n n C3' O3' IU sing 187 n n C3' C2' IU sing 188 n n C3' H3' IU sing 189 n n O3' HO3' IU sing 190 n n C2' O2' IU sing 191 n n C2' C1' IU sing 192 n n C2' H2' IU sing 193 n n O2' HO2' IU sing 194 n n C1' N1 IU sing 195 n n C1' H1' IU sing 196 n n N1 C2 IU sing 197 n n N1 C6 IU sing 198 n n C2 O2 IU doub 199 n n C2 N3 IU sing 200 n n N3 C4 IU sing 201 n n N3 H3 IU sing 202 n n C4 O4 IU doub 203 n n C4 C5 IU sing 204 n n C5 C6 IU doub 205 n n C5 I5 IU sing 206 n n C6 H6 IU sing 207 n n # _atom_sites.entry_id 5KM4 _atom_sites.fract_transf_matrix[1][1] 0.012682 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000883 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021594 _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] 0.015708 _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 IU A 1 201 1 IU IU . D 3 HOH A 1 301 274 HOH HOH . D 3 HOH A 2 302 249 HOH HOH . D 3 HOH A 3 303 158 HOH HOH . D 3 HOH A 4 304 200 HOH HOH . D 3 HOH A 5 305 34 HOH HOH . D 3 HOH A 6 306 22 HOH HOH . D 3 HOH A 7 307 177 HOH HOH . D 3 HOH A 8 308 148 HOH HOH . D 3 HOH A 9 309 260 HOH HOH . D 3 HOH A 10 310 21 HOH HOH . D 3 HOH A 11 311 160 HOH HOH . D 3 HOH A 12 312 147 HOH HOH . D 3 HOH A 13 313 56 HOH HOH . D 3 HOH A 14 314 46 HOH HOH . D 3 HOH A 15 315 275 HOH HOH . D 3 HOH A 16 316 84 HOH HOH . D 3 HOH A 17 317 215 HOH HOH . D 3 HOH A 18 318 139 HOH HOH . D 3 HOH A 19 319 231 HOH HOH . D 3 HOH A 20 320 163 HOH HOH . D 3 HOH A 21 321 45 HOH HOH . D 3 HOH A 22 322 107 HOH HOH . D 3 HOH A 23 323 60 HOH HOH . D 3 HOH A 24 324 7 HOH HOH . D 3 HOH A 25 325 219 HOH HOH . D 3 HOH A 26 326 52 HOH HOH . D 3 HOH A 27 327 173 HOH HOH . D 3 HOH A 28 328 156 HOH HOH . D 3 HOH A 29 329 211 HOH HOH . D 3 HOH A 30 330 110 HOH HOH . D 3 HOH A 31 331 98 HOH HOH . D 3 HOH A 32 332 236 HOH HOH . D 3 HOH A 33 333 91 HOH HOH . D 3 HOH A 34 334 134 HOH HOH . D 3 HOH A 35 335 17 HOH HOH . D 3 HOH A 36 336 108 HOH HOH . D 3 HOH A 37 337 70 HOH HOH . D 3 HOH A 38 338 14 HOH HOH . D 3 HOH A 39 339 95 HOH HOH . D 3 HOH A 40 340 38 HOH HOH . D 3 HOH A 41 341 59 HOH HOH . D 3 HOH A 42 342 42 HOH HOH . D 3 HOH A 43 343 43 HOH HOH . D 3 HOH A 44 344 6 HOH HOH . D 3 HOH A 45 345 218 HOH HOH . D 3 HOH A 46 346 203 HOH HOH . D 3 HOH A 47 347 172 HOH HOH . D 3 HOH A 48 348 12 HOH HOH . D 3 HOH A 49 349 18 HOH HOH . D 3 HOH A 50 350 57 HOH HOH . D 3 HOH A 51 351 112 HOH HOH . D 3 HOH A 52 352 217 HOH HOH . D 3 HOH A 53 353 153 HOH HOH . D 3 HOH A 54 354 159 HOH HOH . D 3 HOH A 55 355 92 HOH HOH . D 3 HOH A 56 356 33 HOH HOH . D 3 HOH A 57 357 120 HOH HOH . D 3 HOH A 58 358 29 HOH HOH . D 3 HOH A 59 359 15 HOH HOH . D 3 HOH A 60 360 136 HOH HOH . D 3 HOH A 61 361 186 HOH HOH . D 3 HOH A 62 362 72 HOH HOH . D 3 HOH A 63 363 137 HOH HOH . D 3 HOH A 64 364 162 HOH HOH . D 3 HOH A 65 365 36 HOH HOH . D 3 HOH A 66 366 135 HOH HOH . D 3 HOH A 67 367 266 HOH HOH . D 3 HOH A 68 368 208 HOH HOH . D 3 HOH A 69 369 5 HOH HOH . D 3 HOH A 70 370 16 HOH HOH . D 3 HOH A 71 371 129 HOH HOH . D 3 HOH A 72 372 209 HOH HOH . D 3 HOH A 73 373 4 HOH HOH . D 3 HOH A 74 374 49 HOH HOH . D 3 HOH A 75 375 109 HOH HOH . D 3 HOH A 76 376 86 HOH HOH . D 3 HOH A 77 377 270 HOH HOH . D 3 HOH A 78 378 47 HOH HOH . D 3 HOH A 79 379 238 HOH HOH . D 3 HOH A 80 380 96 HOH HOH . D 3 HOH A 81 381 178 HOH HOH . D 3 HOH A 82 382 74 HOH HOH . D 3 HOH A 83 383 19 HOH HOH . D 3 HOH A 84 384 115 HOH HOH . D 3 HOH A 85 385 152 HOH HOH . D 3 HOH A 86 386 196 HOH HOH . D 3 HOH A 87 387 75 HOH HOH . D 3 HOH A 88 388 166 HOH HOH . D 3 HOH A 89 389 81 HOH HOH . D 3 HOH A 90 390 54 HOH HOH . D 3 HOH A 91 391 28 HOH HOH . D 3 HOH A 92 392 32 HOH HOH . D 3 HOH A 93 393 37 HOH HOH . D 3 HOH A 94 394 157 HOH HOH . D 3 HOH A 95 395 195 HOH HOH . D 3 HOH A 96 396 185 HOH HOH . D 3 HOH A 97 397 79 HOH HOH . D 3 HOH A 98 398 131 HOH HOH . D 3 HOH A 99 399 67 HOH HOH . D 3 HOH A 100 400 31 HOH HOH . D 3 HOH A 101 401 228 HOH HOH . D 3 HOH A 102 402 161 HOH HOH . D 3 HOH A 103 403 188 HOH HOH . D 3 HOH A 104 404 241 HOH HOH . D 3 HOH A 105 405 210 HOH HOH . D 3 HOH A 106 406 184 HOH HOH . D 3 HOH A 107 407 192 HOH HOH . D 3 HOH A 108 408 187 HOH HOH . D 3 HOH A 109 409 90 HOH HOH . D 3 HOH A 110 410 276 HOH HOH . D 3 HOH A 111 411 93 HOH HOH . D 3 HOH A 112 412 121 HOH HOH . D 3 HOH A 113 413 248 HOH HOH . D 3 HOH A 114 414 261 HOH HOH . D 3 HOH A 115 415 246 HOH HOH . D 3 HOH A 116 416 278 HOH HOH . D 3 HOH A 117 417 133 HOH HOH . D 3 HOH A 118 418 30 HOH HOH . D 3 HOH A 119 419 259 HOH HOH . D 3 HOH A 120 420 100 HOH HOH . D 3 HOH A 121 421 268 HOH HOH . D 3 HOH A 122 422 125 HOH HOH . D 3 HOH A 123 423 181 HOH HOH . D 3 HOH A 124 424 277 HOH HOH . D 3 HOH A 125 425 258 HOH HOH . D 3 HOH A 126 426 252 HOH HOH . D 3 HOH A 127 427 239 HOH HOH . D 3 HOH A 128 428 199 HOH HOH . D 3 HOH A 129 429 243 HOH HOH . D 3 HOH A 130 430 182 HOH HOH . D 3 HOH A 131 431 245 HOH HOH . D 3 HOH A 132 432 250 HOH HOH . D 3 HOH A 133 433 263 HOH HOH . D 3 HOH A 134 434 233 HOH HOH . D 3 HOH A 135 435 58 HOH HOH . D 3 HOH A 136 436 234 HOH HOH . D 3 HOH A 137 437 71 HOH HOH . D 3 HOH A 138 438 214 HOH HOH . D 3 HOH A 139 439 97 HOH HOH . D 3 HOH A 140 440 105 HOH HOH . D 3 HOH A 141 441 61 HOH HOH . D 3 HOH A 142 442 251 HOH HOH . D 3 HOH A 143 443 255 HOH HOH . D 3 HOH A 144 444 94 HOH HOH . D 3 HOH A 145 445 76 HOH HOH . D 3 HOH A 146 446 269 HOH HOH . E 3 HOH B 1 201 73 HOH HOH . E 3 HOH B 2 202 262 HOH HOH . E 3 HOH B 3 203 216 HOH HOH . E 3 HOH B 4 204 8 HOH HOH . E 3 HOH B 5 205 221 HOH HOH . E 3 HOH B 6 206 55 HOH HOH . E 3 HOH B 7 207 35 HOH HOH . E 3 HOH B 8 208 111 HOH HOH . E 3 HOH B 9 209 273 HOH HOH . E 3 HOH B 10 210 212 HOH HOH . E 3 HOH B 11 211 155 HOH HOH . E 3 HOH B 12 212 102 HOH HOH . E 3 HOH B 13 213 171 HOH HOH . E 3 HOH B 14 214 25 HOH HOH . E 3 HOH B 15 215 106 HOH HOH . E 3 HOH B 16 216 48 HOH HOH . E 3 HOH B 17 217 124 HOH HOH . E 3 HOH B 18 218 114 HOH HOH . E 3 HOH B 19 219 169 HOH HOH . E 3 HOH B 20 220 206 HOH HOH . E 3 HOH B 21 221 103 HOH HOH . E 3 HOH B 22 222 227 HOH HOH . E 3 HOH B 23 223 62 HOH HOH . E 3 HOH B 24 224 80 HOH HOH . E 3 HOH B 25 225 235 HOH HOH . E 3 HOH B 26 226 193 HOH HOH . E 3 HOH B 27 227 3 HOH HOH . E 3 HOH B 28 228 44 HOH HOH . E 3 HOH B 29 229 202 HOH HOH . E 3 HOH B 30 230 24 HOH HOH . E 3 HOH B 31 231 50 HOH HOH . E 3 HOH B 32 232 11 HOH HOH . E 3 HOH B 33 233 113 HOH HOH . E 3 HOH B 34 234 2 HOH HOH . E 3 HOH B 35 235 66 HOH HOH . E 3 HOH B 36 236 174 HOH HOH . E 3 HOH B 37 237 23 HOH HOH . E 3 HOH B 38 238 89 HOH HOH . E 3 HOH B 39 239 68 HOH HOH . E 3 HOH B 40 240 167 HOH HOH . E 3 HOH B 41 241 65 HOH HOH . E 3 HOH B 42 242 63 HOH HOH . E 3 HOH B 43 243 205 HOH HOH . E 3 HOH B 44 244 69 HOH HOH . E 3 HOH B 45 245 39 HOH HOH . E 3 HOH B 46 246 198 HOH HOH . E 3 HOH B 47 247 170 HOH HOH . E 3 HOH B 48 248 20 HOH HOH . E 3 HOH B 49 249 51 HOH HOH . E 3 HOH B 50 250 191 HOH HOH . E 3 HOH B 51 251 78 HOH HOH . E 3 HOH B 52 252 13 HOH HOH . E 3 HOH B 53 253 189 HOH HOH . E 3 HOH B 54 254 83 HOH HOH . E 3 HOH B 55 255 85 HOH HOH . E 3 HOH B 56 256 229 HOH HOH . E 3 HOH B 57 257 151 HOH HOH . E 3 HOH B 58 258 240 HOH HOH . E 3 HOH B 59 259 183 HOH HOH . E 3 HOH B 60 260 272 HOH HOH . E 3 HOH B 61 261 64 HOH HOH . E 3 HOH B 62 262 179 HOH HOH . E 3 HOH B 63 263 27 HOH HOH . E 3 HOH B 64 264 104 HOH HOH . E 3 HOH B 65 265 194 HOH HOH . E 3 HOH B 66 266 117 HOH HOH . E 3 HOH B 67 267 149 HOH HOH . E 3 HOH B 68 268 175 HOH HOH . E 3 HOH B 69 269 41 HOH HOH . E 3 HOH B 70 270 197 HOH HOH . E 3 HOH B 71 271 10 HOH HOH . E 3 HOH B 72 272 40 HOH HOH . E 3 HOH B 73 273 26 HOH HOH . E 3 HOH B 74 274 138 HOH HOH . E 3 HOH B 75 275 201 HOH HOH . E 3 HOH B 76 276 127 HOH HOH . E 3 HOH B 77 277 242 HOH HOH . E 3 HOH B 78 278 1 HOH HOH . E 3 HOH B 79 279 165 HOH HOH . E 3 HOH B 80 280 82 HOH HOH . E 3 HOH B 81 281 87 HOH HOH . E 3 HOH B 82 282 53 HOH HOH . E 3 HOH B 83 283 204 HOH HOH . E 3 HOH B 84 284 237 HOH HOH . E 3 HOH B 85 285 264 HOH HOH . E 3 HOH B 86 286 224 HOH HOH . E 3 HOH B 87 287 118 HOH HOH . E 3 HOH B 88 288 254 HOH HOH . E 3 HOH B 89 289 145 HOH HOH . E 3 HOH B 90 290 123 HOH HOH . E 3 HOH B 91 291 253 HOH HOH . E 3 HOH B 92 292 267 HOH HOH . E 3 HOH B 93 293 256 HOH HOH . E 3 HOH B 94 294 142 HOH HOH . E 3 HOH B 95 295 132 HOH HOH . E 3 HOH B 96 296 88 HOH HOH . E 3 HOH B 97 297 265 HOH HOH . E 3 HOH B 98 298 247 HOH HOH . E 3 HOH B 99 299 271 HOH HOH . E 3 HOH B 100 300 130 HOH HOH . E 3 HOH B 101 301 99 HOH HOH . E 3 HOH B 102 302 126 HOH HOH . E 3 HOH B 103 303 128 HOH HOH . E 3 HOH B 104 304 144 HOH HOH . E 3 HOH B 105 305 143 HOH HOH . E 3 HOH B 106 306 146 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 P IU . . . C 2 -32.383 4.832 -23.789 1 11.72 ? P IU 201 A 1 HETATM 2 O OP1 IU . . . C 2 -33.084 3.517 -24.013 1 11.44 ? OP1 IU 201 A 1 HETATM 3 O OP2 IU . . . C 2 -33.021 5.744 -22.763 1 15.57 ? OP2 IU 201 A 1 HETATM 4 O OP3 IU . . . C 2 -30.898 4.656 -23.596 1 14.69 ? OP3 IU 201 A 1 HETATM 5 O O5' IU . . . C 2 -32.53 5.633 -25.158 1 13.92 ? O5' IU 201 A 1 HETATM 6 C C5' IU . . . C 2 -31.939 5.145 -26.36 1 14.62 ? C5' IU 201 A 1 HETATM 7 C C4' IU . . . C 2 -30.598 5.787 -26.628 1 10.32 ? C4' IU 201 A 1 HETATM 8 O O4' IU . . . C 2 -30.058 5.247 -27.87 1 12.81 ? O4' IU 201 A 1 HETATM 9 C C3' IU . . . C 2 -30.637 7.309 -26.8 1 11.89 ? C3' IU 201 A 1 HETATM 10 O O3' IU . . . C 2 -29.487 7.917 -26.188 1 9.93 ? O3' IU 201 A 1 HETATM 11 C C2' IU . . . C 2 -30.604 7.475 -28.322 1 10.83 ? C2' IU 201 A 1 HETATM 12 O O2' IU . . . C 2 -30.108 8.713 -28.796 1 10.95 ? O2' IU 201 A 1 HETATM 13 C C1' IU . . . C 2 -29.727 6.3 -28.744 1 10.56 ? C1' IU 201 A 1 HETATM 14 N N1 IU . . . C 2 -29.993 5.838 -30.107 1 12.71 ? N1 IU 201 A 1 HETATM 15 C C2 IU . . . C 2 -28.951 5.807 -31.036 1 10.01 ? C2 IU 201 A 1 HETATM 16 O O2 IU . . . C 2 -27.792 6.147 -30.716 1 10.16 ? O2 IU 201 A 1 HETATM 17 N N3 IU . . . C 2 -29.214 5.389 -32.281 1 13.91 ? N3 IU 201 A 1 HETATM 18 C C4 IU . . . C 2 -30.456 5.025 -32.648 1 14.24 ? C4 IU 201 A 1 HETATM 19 O O4 IU . . . C 2 -30.645 4.652 -33.831 1 18.1 ? O4 IU 201 A 1 HETATM 20 C C5 IU . . . C 2 -31.577 5.057 -31.671 1 13.99 ? C5 IU 201 A 1 HETATM 21 C C6 IU . . . C 2 -31.254 5.489 -30.4 1 12.72 ? C6 IU 201 A 1 HETATM 22 I I5 IU . . . C 2 -33.551 4.478 -32.165 1 22.51 ? I5 IU 201 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #