data_4QD3 # _model_server_result.job_id exX2itk-NcX2TAwHp1xERg _model_server_result.datetime_utc '2024-12-15 02:39:34' _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 4qd3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4QD3 # _exptl.entry_id 4QD3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 244.205 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-amino-1-(beta-D-ribofuranosyl)-1,3,5-triazin-2(1H)-one _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 4QD3 _cell.length_a 64.111 _cell.length_b 64.111 _cell.length_c 156.62 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4QD3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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,D _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 'C8 H12 N4 O5' _chem_comp.formula_weight 244.205 _chem_comp.id 5AE _chem_comp.mon_nstd_flag . _chem_comp.name 4-amino-1-(beta-D-ribofuranosyl)-1,3,5-triazin-2(1H)-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 5-azacytidine # 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 N4 C4 5AE sing 1 n n N3 C4 5AE doub 2 n n N3 C2 5AE sing 3 n n O2 C2 5AE doub 4 n n C4 N5 5AE sing 5 n n C2 N1 5AE sing 6 n n N5 C6 5AE doub 7 n n N1 C6 5AE sing 8 n n N1 C1' 5AE sing 9 n n O4' C1' 5AE sing 10 n n O4' C4' 5AE sing 11 n n C1' C2' 5AE sing 12 n n C4' C5' 5AE sing 13 n n C4' C3' 5AE sing 14 n n C5' O5' 5AE sing 15 n n C2' O2' 5AE sing 16 n n C2' C3' 5AE sing 17 n n C3' O3' 5AE sing 18 n n N4 H1 5AE sing 19 n n N4 H2 5AE sing 20 n n C6 H3 5AE sing 21 n n C1' H4 5AE sing 22 n n C4' H5 5AE sing 23 n n C5' H6 5AE sing 24 n n C5' H7 5AE sing 25 n n O5' H8 5AE sing 26 n n C3' H9 5AE sing 27 n n O3' H10 5AE sing 28 n n C2' H11 5AE sing 29 n n O2' H12 5AE sing 30 n n # _atom_sites.entry_id 4QD3 _atom_sites.fract_transf_matrix[1][1] 0.015598 _atom_sites.fract_transf_matrix[1][2] 0.009005 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018011 _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] 0.006385 _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 5AE A 1 201 1 5AE ZZZ . C 3 GOL A 1 202 1 GOL GOL . D 4 HOH A 1 301 1 HOH HOH . D 4 HOH A 2 302 2 HOH HOH . D 4 HOH A 3 303 3 HOH HOH . D 4 HOH A 4 304 4 HOH HOH . D 4 HOH A 5 305 5 HOH HOH . D 4 HOH A 6 306 6 HOH HOH . D 4 HOH A 7 307 7 HOH HOH . D 4 HOH A 8 308 8 HOH HOH . D 4 HOH A 9 309 10 HOH HOH . D 4 HOH A 10 310 11 HOH HOH . D 4 HOH A 11 311 12 HOH HOH . D 4 HOH A 12 312 13 HOH HOH . D 4 HOH A 13 313 14 HOH HOH . D 4 HOH A 14 314 15 HOH HOH . D 4 HOH A 15 315 16 HOH HOH . D 4 HOH A 16 316 17 HOH HOH . D 4 HOH A 17 317 18 HOH HOH . D 4 HOH A 18 318 19 HOH HOH . D 4 HOH A 19 319 20 HOH HOH . D 4 HOH A 20 320 21 HOH HOH . D 4 HOH A 21 321 22 HOH HOH . D 4 HOH A 22 322 23 HOH HOH . D 4 HOH A 23 323 24 HOH HOH . D 4 HOH A 24 324 25 HOH HOH . D 4 HOH A 25 325 26 HOH HOH . D 4 HOH A 26 326 27 HOH HOH . D 4 HOH A 27 327 28 HOH HOH . D 4 HOH A 28 328 29 HOH HOH . D 4 HOH A 29 329 30 HOH HOH . D 4 HOH A 30 330 31 HOH HOH . D 4 HOH A 31 331 32 HOH HOH . D 4 HOH A 32 332 33 HOH HOH . D 4 HOH A 33 333 34 HOH HOH . D 4 HOH A 34 334 35 HOH HOH . D 4 HOH A 35 335 36 HOH HOH . D 4 HOH A 36 336 37 HOH HOH . D 4 HOH A 37 337 38 HOH HOH . D 4 HOH A 38 338 39 HOH HOH . D 4 HOH A 39 339 40 HOH HOH . D 4 HOH A 40 340 41 HOH HOH . D 4 HOH A 41 341 42 HOH HOH . D 4 HOH A 42 342 43 HOH HOH . D 4 HOH A 43 343 44 HOH HOH . D 4 HOH A 44 344 45 HOH HOH . D 4 HOH A 45 345 46 HOH HOH . D 4 HOH A 46 346 49 HOH HOH . D 4 HOH A 47 347 50 HOH HOH . D 4 HOH A 48 348 51 HOH HOH . D 4 HOH A 49 349 52 HOH HOH . D 4 HOH A 50 350 53 HOH HOH . D 4 HOH A 51 351 54 HOH HOH . D 4 HOH A 52 352 55 HOH HOH . D 4 HOH A 53 353 56 HOH HOH . D 4 HOH A 54 354 57 HOH HOH . D 4 HOH A 55 355 58 HOH HOH . D 4 HOH A 56 356 59 HOH HOH . D 4 HOH A 57 357 60 HOH HOH . D 4 HOH A 58 358 61 HOH HOH . D 4 HOH A 59 359 62 HOH HOH . D 4 HOH A 60 360 63 HOH HOH . D 4 HOH A 61 361 64 HOH HOH . D 4 HOH A 62 362 65 HOH HOH . D 4 HOH A 63 363 67 HOH HOH . D 4 HOH A 64 364 69 HOH HOH . D 4 HOH A 65 365 70 HOH HOH . D 4 HOH A 66 366 71 HOH HOH . D 4 HOH A 67 367 72 HOH HOH . D 4 HOH A 68 368 73 HOH HOH . D 4 HOH A 69 369 74 HOH HOH . D 4 HOH A 70 370 75 HOH HOH . D 4 HOH A 71 371 76 HOH HOH . D 4 HOH A 72 372 77 HOH HOH . D 4 HOH A 73 373 78 HOH HOH . D 4 HOH A 74 374 79 HOH HOH . D 4 HOH A 75 375 80 HOH HOH . D 4 HOH A 76 376 82 HOH HOH . D 4 HOH A 77 377 83 HOH HOH . D 4 HOH A 78 378 84 HOH HOH . D 4 HOH A 79 379 85 HOH HOH . D 4 HOH A 80 380 86 HOH HOH . D 4 HOH A 81 381 87 HOH HOH . D 4 HOH A 82 382 88 HOH HOH . D 4 HOH A 83 383 89 HOH HOH . D 4 HOH A 84 384 90 HOH HOH . D 4 HOH A 85 385 91 HOH HOH . D 4 HOH A 86 386 92 HOH HOH . D 4 HOH A 87 387 94 HOH HOH . D 4 HOH A 88 388 95 HOH HOH . D 4 HOH A 89 389 96 HOH HOH . D 4 HOH A 90 390 97 HOH HOH . D 4 HOH A 91 391 98 HOH HOH . D 4 HOH A 92 392 99 HOH HOH . D 4 HOH A 93 393 101 HOH HOH . D 4 HOH A 94 394 102 HOH HOH . D 4 HOH A 95 395 103 HOH HOH . D 4 HOH A 96 396 104 HOH HOH . D 4 HOH A 97 397 105 HOH HOH . D 4 HOH A 98 398 106 HOH HOH . D 4 HOH A 99 399 109 HOH HOH . D 4 HOH A 100 400 111 HOH HOH . D 4 HOH A 101 401 112 HOH HOH . D 4 HOH A 102 402 113 HOH HOH . D 4 HOH A 103 403 114 HOH HOH . D 4 HOH A 104 404 115 HOH HOH . D 4 HOH A 105 405 116 HOH HOH . D 4 HOH A 106 406 117 HOH HOH . D 4 HOH A 107 407 120 HOH HOH . D 4 HOH A 108 408 122 HOH HOH . D 4 HOH A 109 409 123 HOH HOH . D 4 HOH A 110 410 124 HOH HOH . D 4 HOH A 111 411 125 HOH HOH . D 4 HOH A 112 412 126 HOH HOH . D 4 HOH A 113 413 127 HOH HOH . D 4 HOH A 114 414 130 HOH HOH . D 4 HOH A 115 415 131 HOH HOH . D 4 HOH A 116 416 132 HOH HOH . D 4 HOH A 117 417 136 HOH HOH . D 4 HOH A 118 418 137 HOH HOH . D 4 HOH A 119 419 141 HOH HOH . D 4 HOH A 120 420 142 HOH HOH . D 4 HOH A 121 421 143 HOH HOH . D 4 HOH A 122 422 144 HOH HOH . D 4 HOH A 123 423 146 HOH HOH . D 4 HOH A 124 424 149 HOH HOH . D 4 HOH A 125 425 152 HOH HOH . D 4 HOH A 126 426 153 HOH HOH . D 4 HOH A 127 427 154 HOH HOH . D 4 HOH A 128 428 157 HOH HOH . D 4 HOH A 129 429 158 HOH HOH . D 4 HOH A 130 430 159 HOH HOH . D 4 HOH A 131 431 160 HOH HOH . D 4 HOH A 132 432 164 HOH HOH . D 4 HOH A 133 433 165 HOH HOH . D 4 HOH A 134 434 166 HOH HOH . D 4 HOH A 135 435 167 HOH HOH . D 4 HOH A 136 436 168 HOH HOH . D 4 HOH A 137 437 169 HOH HOH . D 4 HOH A 138 438 172 HOH HOH . D 4 HOH A 139 439 173 HOH HOH . D 4 HOH A 140 440 175 HOH HOH . D 4 HOH A 141 441 176 HOH HOH . D 4 HOH A 142 442 177 HOH HOH . D 4 HOH A 143 443 178 HOH HOH . D 4 HOH A 144 444 179 HOH HOH . D 4 HOH A 145 445 180 HOH HOH . D 4 HOH A 146 446 181 HOH HOH . D 4 HOH A 147 447 182 HOH HOH . D 4 HOH A 148 448 183 HOH HOH . D 4 HOH A 149 449 184 HOH HOH . D 4 HOH A 150 450 185 HOH HOH . D 4 HOH A 151 451 186 HOH HOH . D 4 HOH A 152 452 187 HOH HOH . D 4 HOH A 153 453 188 HOH HOH . D 4 HOH A 154 454 189 HOH HOH . D 4 HOH A 155 455 190 HOH HOH . D 4 HOH A 156 456 193 HOH HOH . D 4 HOH A 157 457 196 HOH HOH . D 4 HOH A 158 458 197 HOH HOH . D 4 HOH A 159 459 199 HOH HOH . D 4 HOH A 160 460 201 HOH HOH . D 4 HOH A 161 461 202 HOH HOH . D 4 HOH A 162 462 203 HOH HOH . D 4 HOH A 163 463 204 HOH HOH . D 4 HOH A 164 464 205 HOH HOH . D 4 HOH A 165 465 207 HOH HOH . D 4 HOH A 166 466 208 HOH HOH . D 4 HOH A 167 467 209 HOH HOH . D 4 HOH A 168 468 210 HOH HOH . D 4 HOH A 169 469 211 HOH HOH . D 4 HOH A 170 470 212 HOH HOH . D 4 HOH A 171 471 213 HOH HOH . D 4 HOH A 172 472 214 HOH HOH . D 4 HOH A 173 473 215 HOH HOH . D 4 HOH A 174 474 216 HOH HOH . D 4 HOH A 175 475 217 HOH HOH . D 4 HOH A 176 476 218 HOH HOH . D 4 HOH A 177 477 219 HOH HOH . D 4 HOH A 178 478 220 HOH HOH . D 4 HOH A 179 479 221 HOH HOH . D 4 HOH A 180 480 222 HOH HOH . D 4 HOH A 181 481 223 HOH HOH . D 4 HOH A 182 482 224 HOH HOH . D 4 HOH A 183 483 225 HOH HOH . D 4 HOH A 184 484 226 HOH HOH . D 4 HOH A 185 485 227 HOH HOH . D 4 HOH A 186 486 228 HOH HOH . D 4 HOH A 187 487 229 HOH HOH . D 4 HOH A 188 488 233 HOH HOH . D 4 HOH A 189 489 234 HOH HOH . D 4 HOH A 190 490 235 HOH HOH . D 4 HOH A 191 491 236 HOH HOH . D 4 HOH A 192 492 1 HOH HOH . D 4 HOH A 193 493 2 HOH HOH . D 4 HOH A 194 494 3 HOH HOH . D 4 HOH A 195 495 4 HOH HOH . D 4 HOH A 196 496 5 HOH HOH . D 4 HOH A 197 497 1 HOH HOH . D 4 HOH A 198 498 2 HOH HOH . D 4 HOH A 199 499 3 HOH HOH . D 4 HOH A 200 500 4 HOH HOH . D 4 HOH A 201 501 1 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 O O2 5AE . . . B 2 -5.831 15.81 5.854 1 24.06 ? O2 5AE 201 A 1 HETATM 2 C C2 5AE . . . B 2 -7.019 15.549 6.11 1 26.38 ? C2 5AE 201 A 1 HETATM 3 N N3 5AE . . . B 2 -7.969 16.401 5.663 1 26.77 ? N3 5AE 201 A 1 HETATM 4 C C4 5AE . . . B 2 -9.264 16.163 5.934 1 27.37 ? C4 5AE 201 A 1 HETATM 5 N N4 5AE . . . B 2 -10.195 17.025 5.476 1 27.45 ? N4 5AE 201 A 1 HETATM 6 N N5 5AE . . . B 2 -9.616 15.06 6.655 1 28.2 ? N5 5AE 201 A 1 HETATM 7 N N1 5AE . . . B 2 -7.365 14.452 6.826 1 26.29 ? N1 5AE 201 A 1 HETATM 8 C C6 5AE . . . B 2 -8.664 14.22 7.092 1 26.5 ? C6 5AE 201 A 1 HETATM 9 C C1' 5AE . . . B 2 -6.325 13.532 7.319 1 25.9 ? C1' 5AE 201 A 1 HETATM 10 O O4' 5AE . . . B 2 -6.646 12.158 7.065 1 25.91 ? O4' 5AE 201 A 1 HETATM 11 C C4' 5AE . . . B 2 -5.858 11.393 7.975 1 25.92 ? C4' 5AE 201 A 1 HETATM 12 C C5' 5AE . . . B 2 -6.382 9.964 8.086 1 26.49 ? C5' 5AE 201 A 1 HETATM 13 O O5' 5AE . . . B 2 -7.738 9.954 8.554 1 26.06 ? O5' 5AE 201 A 1 HETATM 14 C C3' 5AE . . . B 2 -5.894 12.191 9.275 1 25.91 ? C3' 5AE 201 A 1 HETATM 15 O O3' 5AE . . . B 2 -4.689 12.037 10.026 1 25.91 ? O3' 5AE 201 A 1 HETATM 16 C C2' 5AE . . . B 2 -6.114 13.633 8.831 1 26.21 ? C2' 5AE 201 A 1 HETATM 17 O O2' 5AE . . . B 2 -4.989 14.473 9.163 1 26.44 ? O2' 5AE 201 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 17 #