data_4LM7 # _model_server_result.job_id duMtR5ARxVBqXD7dppVDoA _model_server_result.datetime_utc '2025-02-27 01:33:12' _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 4lm7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4LM7 # _exptl.entry_id 4LM7 _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 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 4LM7 _cell.length_a 81.94 _cell.length_b 81.94 _cell.length_c 42.82 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LM7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 326 n n N1 C6 U5P sing 327 n n N1 C1' U5P sing 328 n n C2 N3 U5P sing 329 n n C2 O2 U5P doub 330 n n N3 C4 U5P sing 331 n n N3 HN3 U5P sing 332 n n C4 C5 U5P sing 333 n n C4 O4 U5P doub 334 n n C5 C6 U5P doub 335 n n C5 H5 U5P sing 336 n n C6 H6 U5P sing 337 n n C1' C2' U5P sing 338 n n C1' O4' U5P sing 339 n n C1' H1' U5P sing 340 n n C2' O2' U5P sing 341 n n C2' C3' U5P sing 342 n n C2' H2' U5P sing 343 n n O2' HO2' U5P sing 344 n n C3' C4' U5P sing 345 n n C3' O3' U5P sing 346 n n C3' H3' U5P sing 347 n n C4' O4' U5P sing 348 n n C4' C5' U5P sing 349 n n C4' H4' U5P sing 350 n n O3' HO3' U5P sing 351 n n C5' O5' U5P sing 352 n n C5' "H5'1" U5P sing 353 n n C5' "H5'2" U5P sing 354 n n O5' P U5P sing 355 n n P O1P U5P doub 356 n n P O2P U5P sing 357 n n P O3P U5P sing 358 n n O2P HOP2 U5P sing 359 n n O3P HOP3 U5P sing 360 n n # _atom_sites.entry_id 4LM7 _atom_sites.fract_transf_matrix[1][1] 0.012204 _atom_sites.fract_transf_matrix[1][2] 0.007046 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014092 _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] 0.023354 _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 U5P A 1 201 192 U5P DRG . C 3 HOH A 1 301 193 HOH HOH . C 3 HOH A 2 302 194 HOH HOH . C 3 HOH A 3 303 195 HOH HOH . C 3 HOH A 4 304 196 HOH HOH . C 3 HOH A 5 305 197 HOH HOH . C 3 HOH A 6 306 200 HOH HOH . C 3 HOH A 7 307 201 HOH HOH . C 3 HOH A 8 308 202 HOH HOH . C 3 HOH A 9 309 203 HOH HOH . C 3 HOH A 10 310 204 HOH HOH . C 3 HOH A 11 311 205 HOH HOH . C 3 HOH A 12 312 206 HOH HOH . C 3 HOH A 13 313 207 HOH HOH . C 3 HOH A 14 314 208 HOH HOH . C 3 HOH A 15 315 209 HOH HOH . C 3 HOH A 16 316 210 HOH HOH . C 3 HOH A 17 317 211 HOH HOH . C 3 HOH A 18 318 212 HOH HOH . C 3 HOH A 19 319 214 HOH HOH . C 3 HOH A 20 320 215 HOH HOH . C 3 HOH A 21 321 216 HOH HOH . C 3 HOH A 22 322 217 HOH HOH . C 3 HOH A 23 323 218 HOH HOH . C 3 HOH A 24 324 219 HOH HOH . C 3 HOH A 25 325 220 HOH HOH . C 3 HOH A 26 326 221 HOH HOH . C 3 HOH A 27 327 222 HOH HOH . C 3 HOH A 28 328 223 HOH HOH . C 3 HOH A 29 329 224 HOH HOH . C 3 HOH A 30 330 225 HOH HOH . C 3 HOH A 31 331 226 HOH HOH . C 3 HOH A 32 332 227 HOH HOH . C 3 HOH A 33 333 229 HOH HOH . C 3 HOH A 34 334 231 HOH HOH . C 3 HOH A 35 335 232 HOH HOH . C 3 HOH A 36 336 233 HOH HOH . C 3 HOH A 37 337 234 HOH HOH . C 3 HOH A 38 338 235 HOH HOH . C 3 HOH A 39 339 236 HOH HOH . C 3 HOH A 40 340 237 HOH HOH . C 3 HOH A 41 341 238 HOH HOH . C 3 HOH A 42 342 239 HOH HOH . C 3 HOH A 43 343 240 HOH HOH . C 3 HOH A 44 344 241 HOH HOH . C 3 HOH A 45 345 245 HOH HOH . C 3 HOH A 46 346 246 HOH HOH . C 3 HOH A 47 347 247 HOH HOH . C 3 HOH A 48 348 248 HOH HOH . C 3 HOH A 49 349 249 HOH HOH . C 3 HOH A 50 350 250 HOH HOH . C 3 HOH A 51 351 251 HOH HOH . C 3 HOH A 52 352 252 HOH HOH . C 3 HOH A 53 353 253 HOH HOH . C 3 HOH A 54 354 254 HOH HOH . C 3 HOH A 55 355 255 HOH HOH . C 3 HOH A 56 356 256 HOH HOH . C 3 HOH A 57 357 257 HOH HOH . C 3 HOH A 58 358 258 HOH HOH . C 3 HOH A 59 359 259 HOH HOH . C 3 HOH A 60 360 260 HOH HOH . C 3 HOH A 61 361 261 HOH HOH . C 3 HOH A 62 362 262 HOH HOH . C 3 HOH A 63 363 263 HOH HOH . C 3 HOH A 64 364 264 HOH HOH . C 3 HOH A 65 365 265 HOH HOH . C 3 HOH A 66 366 266 HOH HOH . C 3 HOH A 67 367 267 HOH HOH . C 3 HOH A 68 368 268 HOH HOH . C 3 HOH A 69 369 269 HOH HOH . C 3 HOH A 70 370 270 HOH HOH . C 3 HOH A 71 371 271 HOH HOH . C 3 HOH A 72 372 272 HOH HOH . C 3 HOH A 73 373 273 HOH HOH . C 3 HOH A 74 374 274 HOH HOH . C 3 HOH A 75 375 275 HOH HOH . C 3 HOH A 76 376 276 HOH HOH . C 3 HOH A 77 377 277 HOH HOH . C 3 HOH A 78 378 279 HOH HOH . C 3 HOH A 79 379 281 HOH HOH . C 3 HOH A 80 380 283 HOH HOH . C 3 HOH A 81 381 284 HOH HOH . C 3 HOH A 82 382 285 HOH HOH . C 3 HOH A 83 383 286 HOH HOH . C 3 HOH A 84 384 287 HOH HOH . C 3 HOH A 85 385 288 HOH HOH . C 3 HOH A 86 386 290 HOH HOH . C 3 HOH A 87 387 291 HOH HOH . C 3 HOH A 88 388 292 HOH HOH . C 3 HOH A 89 389 293 HOH HOH . C 3 HOH A 90 390 294 HOH HOH . C 3 HOH A 91 391 296 HOH HOH . C 3 HOH A 92 392 297 HOH HOH . C 3 HOH A 93 393 298 HOH HOH . C 3 HOH A 94 394 299 HOH HOH . C 3 HOH A 95 395 300 HOH HOH . C 3 HOH A 96 396 301 HOH HOH . C 3 HOH A 97 397 302 HOH HOH . C 3 HOH A 98 398 303 HOH HOH . C 3 HOH A 99 399 304 HOH HOH . C 3 HOH A 100 400 305 HOH HOH . C 3 HOH A 101 401 306 HOH HOH . C 3 HOH A 102 402 307 HOH HOH . C 3 HOH A 103 403 308 HOH HOH . C 3 HOH A 104 404 309 HOH HOH . C 3 HOH A 105 405 310 HOH HOH . C 3 HOH A 106 406 311 HOH HOH . C 3 HOH A 107 407 312 HOH HOH . C 3 HOH A 108 408 313 HOH HOH . C 3 HOH A 109 409 314 HOH HOH . C 3 HOH A 110 410 315 HOH HOH . C 3 HOH A 111 411 316 HOH HOH . C 3 HOH A 112 412 317 HOH HOH . C 3 HOH A 113 413 318 HOH HOH . C 3 HOH A 114 414 319 HOH HOH . C 3 HOH A 115 415 320 HOH HOH . C 3 HOH A 116 416 321 HOH HOH . C 3 HOH A 117 417 322 HOH HOH . C 3 HOH A 118 418 323 HOH HOH . C 3 HOH A 119 419 324 HOH HOH . C 3 HOH A 120 420 326 HOH HOH . C 3 HOH A 121 421 327 HOH HOH . C 3 HOH A 122 422 328 HOH HOH . C 3 HOH A 123 423 329 HOH HOH . C 3 HOH A 124 424 330 HOH HOH . C 3 HOH A 125 425 331 HOH HOH . C 3 HOH A 126 426 332 HOH HOH . C 3 HOH A 127 427 333 HOH HOH . C 3 HOH A 128 428 334 HOH HOH . C 3 HOH A 129 429 335 HOH HOH . C 3 HOH A 130 430 336 HOH HOH . C 3 HOH A 131 431 337 HOH HOH . C 3 HOH A 132 432 338 HOH HOH . C 3 HOH A 133 433 339 HOH HOH . C 3 HOH A 134 434 341 HOH HOH . C 3 HOH A 135 435 342 HOH HOH . C 3 HOH A 136 436 343 HOH HOH . C 3 HOH A 137 437 344 HOH HOH . C 3 HOH A 138 438 345 HOH HOH . C 3 HOH A 139 439 346 HOH HOH . C 3 HOH A 140 440 347 HOH HOH . C 3 HOH A 141 441 348 HOH HOH . C 3 HOH A 142 442 349 HOH HOH . C 3 HOH A 143 443 350 HOH HOH . C 3 HOH A 144 444 352 HOH HOH . C 3 HOH A 145 445 353 HOH HOH . C 3 HOH A 146 446 354 HOH HOH . C 3 HOH A 147 447 355 HOH HOH . C 3 HOH A 148 448 356 HOH HOH . C 3 HOH A 149 449 357 HOH HOH . C 3 HOH A 150 450 358 HOH HOH . C 3 HOH A 151 451 359 HOH HOH . C 3 HOH A 152 452 360 HOH HOH . C 3 HOH A 153 453 362 HOH HOH . C 3 HOH A 154 454 363 HOH HOH . C 3 HOH A 155 455 364 HOH HOH . C 3 HOH A 156 456 365 HOH HOH . C 3 HOH A 157 457 366 HOH HOH . C 3 HOH A 158 458 370 HOH HOH . C 3 HOH A 159 459 372 HOH HOH . C 3 HOH A 160 460 373 HOH HOH . C 3 HOH A 161 461 374 HOH HOH . C 3 HOH A 162 462 375 HOH HOH . C 3 HOH A 163 463 377 HOH HOH . C 3 HOH A 164 464 379 HOH HOH . C 3 HOH A 165 465 381 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 U5P . . . B 2 2.58 -26.593 0.097 1 44.23 ? N1 U5P 201 A 1 HETATM 2 C C2 U5P . . . B 2 3.75 -26.832 0.836 1 44.62 ? C2 U5P 201 A 1 HETATM 3 N N3 U5P . . . B 2 4.035 -28.022 1.099 1 45.86 ? N3 U5P 201 A 1 HETATM 4 C C4 U5P . . . B 2 3.604 -29.03 0.208 1 45.29 ? C4 U5P 201 A 1 HETATM 5 C C5 U5P . . . B 2 2.879 -28.692 -0.967 1 45.31 ? C5 U5P 201 A 1 HETATM 6 C C6 U5P . . . B 2 2.534 -27.375 -1.129 1 44.73 ? C6 U5P 201 A 1 HETATM 7 O O2 U5P . . . B 2 4.503 -25.777 1.157 1 42.86 ? O2 U5P 201 A 1 HETATM 8 O O4 U5P . . . B 2 3.939 -30.488 0.518 1 46.69 ? O4 U5P 201 A 1 HETATM 9 C C1' U5P . . . B 2 2.247 -25.197 -0.18 1 46.05 ? C1' U5P 201 A 1 HETATM 10 C C2' U5P . . . B 2 0.81 -24.957 -0.609 1 43.9 ? C2' U5P 201 A 1 HETATM 11 O O2' U5P . . . B 2 0.574 -25.395 -1.927 1 47.68 ? O2' U5P 201 A 1 HETATM 12 C C3' U5P . . . B 2 0.752 -23.446 -0.419 1 47.32 ? C3' U5P 201 A 1 HETATM 13 C C4' U5P . . . B 2 1.498 -23.263 0.897 1 46.46 ? C4' U5P 201 A 1 HETATM 14 O O3' U5P . . . B 2 1.52 -22.816 -1.452 1 48.23 ? O3' U5P 201 A 1 HETATM 15 O O4' U5P . . . B 2 2.395 -24.413 0.998 1 47.44 ? O4' U5P 201 A 1 HETATM 16 C C5' U5P . . . B 2 0.608 -23.152 2.105 1 45.93 ? C5' U5P 201 A 1 HETATM 17 O O5' U5P . . . B 2 0.807 -24.198 3.049 1 49.43 ? O5' U5P 201 A 1 HETATM 18 P P U5P . . . B 2 -0.19 -24.334 4.294 1 48.49 ? P U5P 201 A 1 HETATM 19 O O1P U5P . . . B 2 -1.387 -23.34 4.022 1 49.36 ? O1P U5P 201 A 1 HETATM 20 O O2P U5P . . . B 2 -0.491 -25.718 4.454 1 51.51 ? O2P U5P 201 A 1 HETATM 21 O O3P U5P . . . B 2 0.443 -24.003 5.614 1 49.92 ? O3P U5P 201 A 1 HETATM 22 H H1' U5P . . . B 2 2.823 -24.832 -0.917 1 46.05 ? H1' U5P 201 A 1 HETATM 23 H H2' U5P . . . B 2 0.284 -25.331 -0.079 1 43.9 ? H2' U5P 201 A 1 HETATM 24 H HO2' U5P . . . B 2 -0.185 -25.738 -1.987 1 47.68 ? HO2' U5P 201 A 1 HETATM 25 H H3' U5P . . . B 2 -0.086 -23.088 -0.385 1 47.32 ? H3' U5P 201 A 1 HETATM 26 H H4' U5P . . . B 2 2.041 -22.381 0.861 1 46.46 ? H4' U5P 201 A 1 HETATM 27 H HO3' U5P . . . B 2 1.018 -22.668 -2.172 1 48.23 ? HO3' U5P 201 A 1 HETATM 28 H "H5'1" U5P . . . B 2 -0.352 -23.206 1.703 1 45.93 ? "H5'1" U5P 201 A 1 HETATM 29 H "H5'2" U5P . . . B 2 0.875 -22.138 2.468 1 45.93 ? "H5'2" U5P 201 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #