data_5Y9A # _model_server_result.job_id p7kRb6KhFINAegMTPsxKng _model_server_result.datetime_utc '2024-11-23 11:50:15' _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 5y9a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5Y9A # _exptl.entry_id 5Y9A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 243.217 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description CYTARABINE _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 90 _cell.entry_id 5Y9A _cell.length_a 34 _cell.length_b 66.16 _cell.length_c 76.15 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y9A _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 'C9 H13 N3 O5' _chem_comp.formula_weight 243.217 _chem_comp.id AR3 _chem_comp.mon_nstd_flag . _chem_comp.name CYTARABINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1-BETA-D-ARABINOFURANOSYLCYTOSINE;ARA-C # 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 O5' C5' AR3 sing 13 n n O5' H5' AR3 sing 14 n n C5' C4' AR3 sing 15 n n C5' "H5'1" AR3 sing 16 n n C5' "H5'2" AR3 sing 17 n n C4' O4' AR3 sing 18 n n C4' C3' AR3 sing 19 n n C4' H4' AR3 sing 20 n n O4' C1' AR3 sing 21 n n C1' N1 AR3 sing 22 n n C1' C2' AR3 sing 23 n n C1' H1' AR3 sing 24 n n N1 C6 AR3 sing 25 n y N1 C2 AR3 sing 26 n y C6 C5 AR3 doub 27 n y C6 H6 AR3 sing 28 n n C5 C4 AR3 sing 29 n y C5 H5 AR3 sing 30 n n C4 N3 AR3 doub 31 n y C4 N4 AR3 sing 32 n n N3 C2 AR3 sing 33 n y C2 O2 AR3 doub 34 n n N4 HN41 AR3 sing 35 n n N4 HN42 AR3 sing 36 n n C2' O1 AR3 sing 37 n n C2' C3' AR3 sing 38 n n C2' H2' AR3 sing 39 n n O1 HO1 AR3 sing 40 n n C3' O3' AR3 sing 41 n n C3' H3' AR3 sing 42 n n O3' H1 AR3 sing 43 n n # _atom_sites.entry_id 5Y9A _atom_sites.fract_transf_matrix[1][1] 0.029412 _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] 0.015115 _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] 0.013132 _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 AR3 A 1 201 201 AR3 AR3 . C 3 PO4 A 1 202 202 PO4 PO4 . D 4 HOH A 1 301 395 HOH HOH . D 4 HOH A 2 302 499 HOH HOH . D 4 HOH A 3 303 527 HOH HOH . D 4 HOH A 4 304 466 HOH HOH . D 4 HOH A 5 305 384 HOH HOH . D 4 HOH A 6 306 468 HOH HOH . D 4 HOH A 7 307 358 HOH HOH . D 4 HOH A 8 308 493 HOH HOH . D 4 HOH A 9 309 406 HOH HOH . D 4 HOH A 10 310 418 HOH HOH . D 4 HOH A 11 311 448 HOH HOH . D 4 HOH A 12 312 316 HOH HOH . D 4 HOH A 13 313 485 HOH HOH . D 4 HOH A 14 314 513 HOH HOH . D 4 HOH A 15 315 534 HOH HOH . D 4 HOH A 16 316 380 HOH HOH . D 4 HOH A 17 317 378 HOH HOH . D 4 HOH A 18 318 531 HOH HOH . D 4 HOH A 19 319 339 HOH HOH . D 4 HOH A 20 320 535 HOH HOH . D 4 HOH A 21 321 333 HOH HOH . D 4 HOH A 22 322 509 HOH HOH . D 4 HOH A 23 323 506 HOH HOH . D 4 HOH A 24 324 502 HOH HOH . D 4 HOH A 25 325 424 HOH HOH . D 4 HOH A 26 326 417 HOH HOH . D 4 HOH A 27 327 407 HOH HOH . D 4 HOH A 28 328 368 HOH HOH . D 4 HOH A 29 329 341 HOH HOH . D 4 HOH A 30 330 432 HOH HOH . D 4 HOH A 31 331 401 HOH HOH . D 4 HOH A 32 332 539 HOH HOH . D 4 HOH A 33 333 382 HOH HOH . D 4 HOH A 34 334 374 HOH HOH . D 4 HOH A 35 335 309 HOH HOH . D 4 HOH A 36 336 436 HOH HOH . D 4 HOH A 37 337 305 HOH HOH . D 4 HOH A 38 338 376 HOH HOH . D 4 HOH A 39 339 477 HOH HOH . D 4 HOH A 40 340 389 HOH HOH . D 4 HOH A 41 341 446 HOH HOH . D 4 HOH A 42 342 318 HOH HOH . D 4 HOH A 43 343 366 HOH HOH . D 4 HOH A 44 344 402 HOH HOH . D 4 HOH A 45 345 455 HOH HOH . D 4 HOH A 46 346 301 HOH HOH . D 4 HOH A 47 347 452 HOH HOH . D 4 HOH A 48 348 346 HOH HOH . D 4 HOH A 49 349 425 HOH HOH . D 4 HOH A 50 350 538 HOH HOH . D 4 HOH A 51 351 350 HOH HOH . D 4 HOH A 52 352 321 HOH HOH . D 4 HOH A 53 353 334 HOH HOH . D 4 HOH A 54 354 409 HOH HOH . D 4 HOH A 55 355 510 HOH HOH . D 4 HOH A 56 356 449 HOH HOH . D 4 HOH A 57 357 304 HOH HOH . D 4 HOH A 58 358 457 HOH HOH . D 4 HOH A 59 359 332 HOH HOH . D 4 HOH A 60 360 430 HOH HOH . D 4 HOH A 61 361 340 HOH HOH . D 4 HOH A 62 362 405 HOH HOH . D 4 HOH A 63 363 427 HOH HOH . D 4 HOH A 64 364 323 HOH HOH . D 4 HOH A 65 365 336 HOH HOH . D 4 HOH A 66 366 342 HOH HOH . D 4 HOH A 67 367 421 HOH HOH . D 4 HOH A 68 368 308 HOH HOH . D 4 HOH A 69 369 354 HOH HOH . D 4 HOH A 70 370 441 HOH HOH . D 4 HOH A 71 371 458 HOH HOH . D 4 HOH A 72 372 322 HOH HOH . D 4 HOH A 73 373 319 HOH HOH . D 4 HOH A 74 374 317 HOH HOH . D 4 HOH A 75 375 352 HOH HOH . D 4 HOH A 76 376 377 HOH HOH . D 4 HOH A 77 377 320 HOH HOH . D 4 HOH A 78 378 363 HOH HOH . D 4 HOH A 79 379 310 HOH HOH . D 4 HOH A 80 380 367 HOH HOH . D 4 HOH A 81 381 397 HOH HOH . D 4 HOH A 82 382 413 HOH HOH . D 4 HOH A 83 383 444 HOH HOH . D 4 HOH A 84 384 399 HOH HOH . D 4 HOH A 85 385 415 HOH HOH . D 4 HOH A 86 386 302 HOH HOH . D 4 HOH A 87 387 335 HOH HOH . D 4 HOH A 88 388 307 HOH HOH . D 4 HOH A 89 389 431 HOH HOH . D 4 HOH A 90 390 356 HOH HOH . D 4 HOH A 91 391 394 HOH HOH . D 4 HOH A 92 392 369 HOH HOH . D 4 HOH A 93 393 528 HOH HOH . D 4 HOH A 94 394 517 HOH HOH . D 4 HOH A 95 395 442 HOH HOH . D 4 HOH A 96 396 428 HOH HOH . D 4 HOH A 97 397 337 HOH HOH . D 4 HOH A 98 398 348 HOH HOH . D 4 HOH A 99 399 414 HOH HOH . D 4 HOH A 100 400 330 HOH HOH . D 4 HOH A 101 401 408 HOH HOH . D 4 HOH A 102 402 349 HOH HOH . D 4 HOH A 103 403 303 HOH HOH . D 4 HOH A 104 404 325 HOH HOH . D 4 HOH A 105 405 327 HOH HOH . D 4 HOH A 106 406 410 HOH HOH . D 4 HOH A 107 407 445 HOH HOH . D 4 HOH A 108 408 435 HOH HOH . D 4 HOH A 109 409 365 HOH HOH . D 4 HOH A 110 410 375 HOH HOH . D 4 HOH A 111 411 357 HOH HOH . D 4 HOH A 112 412 328 HOH HOH . D 4 HOH A 113 413 324 HOH HOH . D 4 HOH A 114 414 364 HOH HOH . D 4 HOH A 115 415 370 HOH HOH . D 4 HOH A 116 416 326 HOH HOH . D 4 HOH A 117 417 511 HOH HOH . D 4 HOH A 118 418 329 HOH HOH . D 4 HOH A 119 419 387 HOH HOH . D 4 HOH A 120 420 360 HOH HOH . D 4 HOH A 121 421 486 HOH HOH . D 4 HOH A 122 422 311 HOH HOH . D 4 HOH A 123 423 494 HOH HOH . D 4 HOH A 124 424 422 HOH HOH . D 4 HOH A 125 425 403 HOH HOH . D 4 HOH A 126 426 312 HOH HOH . D 4 HOH A 127 427 386 HOH HOH . D 4 HOH A 128 428 514 HOH HOH . D 4 HOH A 129 429 453 HOH HOH . D 4 HOH A 130 430 440 HOH HOH . D 4 HOH A 131 431 497 HOH HOH . D 4 HOH A 132 432 338 HOH HOH . D 4 HOH A 133 433 362 HOH HOH . D 4 HOH A 134 434 1 HOH HOH . D 4 HOH A 135 435 503 HOH HOH . D 4 HOH A 136 436 429 HOH HOH . D 4 HOH A 137 437 385 HOH HOH . D 4 HOH A 138 438 392 HOH HOH . D 4 HOH A 139 439 450 HOH HOH . D 4 HOH A 140 440 313 HOH HOH . D 4 HOH A 141 441 345 HOH HOH . D 4 HOH A 142 442 306 HOH HOH . D 4 HOH A 143 443 331 HOH HOH . D 4 HOH A 144 444 438 HOH HOH . D 4 HOH A 145 445 454 HOH HOH . D 4 HOH A 146 446 315 HOH HOH . D 4 HOH A 147 447 404 HOH HOH . D 4 HOH A 148 448 437 HOH HOH . D 4 HOH A 149 449 447 HOH HOH . D 4 HOH A 150 450 355 HOH HOH . D 4 HOH A 151 451 390 HOH HOH . D 4 HOH A 152 452 411 HOH HOH . D 4 HOH A 153 453 500 HOH HOH . D 4 HOH A 154 454 359 HOH HOH . D 4 HOH A 155 455 353 HOH HOH . D 4 HOH A 156 456 443 HOH HOH . D 4 HOH A 157 457 520 HOH HOH . D 4 HOH A 158 458 314 HOH HOH . D 4 HOH A 159 459 491 HOH HOH . D 4 HOH A 160 460 516 HOH HOH . D 4 HOH A 161 461 525 HOH HOH . D 4 HOH A 162 462 504 HOH HOH . D 4 HOH A 163 463 542 HOH HOH . D 4 HOH A 164 464 451 HOH HOH . D 4 HOH A 165 465 512 HOH HOH . D 4 HOH A 166 466 393 HOH HOH . D 4 HOH A 167 467 3 HOH HOH . D 4 HOH A 168 468 343 HOH HOH . D 4 HOH A 169 469 487 HOH HOH . D 4 HOH A 170 470 434 HOH HOH . D 4 HOH A 171 471 505 HOH HOH . D 4 HOH A 172 472 381 HOH HOH . D 4 HOH A 173 473 501 HOH HOH . D 4 HOH A 174 474 507 HOH HOH . D 4 HOH A 175 475 426 HOH HOH . D 4 HOH A 176 476 439 HOH HOH . D 4 HOH A 177 477 391 HOH HOH . D 4 HOH A 178 478 398 HOH HOH . D 4 HOH A 179 479 347 HOH HOH . D 4 HOH A 180 480 400 HOH HOH . D 4 HOH A 181 481 459 HOH HOH . D 4 HOH A 182 482 433 HOH HOH . D 4 HOH A 183 483 464 HOH HOH . D 4 HOH A 184 484 361 HOH HOH . D 4 HOH A 185 485 495 HOH HOH . D 4 HOH A 186 486 462 HOH HOH . D 4 HOH A 187 487 515 HOH HOH . D 4 HOH A 188 488 540 HOH HOH . D 4 HOH A 189 489 420 HOH HOH . D 4 HOH A 190 490 416 HOH HOH . D 4 HOH A 191 491 344 HOH HOH . D 4 HOH A 192 492 483 HOH HOH . D 4 HOH A 193 493 461 HOH HOH . D 4 HOH A 194 494 396 HOH HOH . D 4 HOH A 195 495 351 HOH HOH . D 4 HOH A 196 496 518 HOH HOH . D 4 HOH A 197 497 488 HOH HOH . D 4 HOH A 198 498 536 HOH HOH . D 4 HOH A 199 499 467 HOH HOH . D 4 HOH A 200 500 508 HOH HOH . D 4 HOH A 201 501 460 HOH HOH . D 4 HOH A 202 502 472 HOH HOH . D 4 HOH A 203 503 479 HOH HOH . D 4 HOH A 204 504 379 HOH HOH . D 4 HOH A 205 505 469 HOH HOH . D 4 HOH A 206 506 492 HOH HOH . D 4 HOH A 207 507 529 HOH HOH . D 4 HOH A 208 508 465 HOH HOH . D 4 HOH A 209 509 388 HOH HOH . D 4 HOH A 210 510 371 HOH HOH . D 4 HOH A 211 511 473 HOH HOH . D 4 HOH A 212 512 475 HOH HOH . D 4 HOH A 213 513 456 HOH HOH . D 4 HOH A 214 514 474 HOH HOH . D 4 HOH A 215 515 373 HOH HOH . D 4 HOH A 216 516 537 HOH HOH . D 4 HOH A 217 517 412 HOH HOH . D 4 HOH A 218 518 478 HOH HOH . D 4 HOH A 219 519 490 HOH HOH . D 4 HOH A 220 520 541 HOH HOH . D 4 HOH A 221 521 482 HOH HOH . D 4 HOH A 222 522 2 HOH HOH . D 4 HOH A 223 523 423 HOH HOH . D 4 HOH A 224 524 372 HOH HOH . D 4 HOH A 225 525 533 HOH HOH . D 4 HOH A 226 526 496 HOH HOH . D 4 HOH A 227 527 481 HOH HOH . D 4 HOH A 228 528 498 HOH HOH . D 4 HOH A 229 529 532 HOH HOH . D 4 HOH A 230 530 521 HOH HOH . D 4 HOH A 231 531 526 HOH HOH . D 4 HOH A 232 532 530 HOH HOH . D 4 HOH A 233 533 523 HOH HOH . D 4 HOH A 234 534 471 HOH HOH . D 4 HOH A 235 535 484 HOH HOH . D 4 HOH A 236 536 480 HOH HOH . D 4 HOH A 237 537 524 HOH HOH . D 4 HOH A 238 538 519 HOH HOH . D 4 HOH A 239 539 383 HOH HOH . D 4 HOH A 240 540 463 HOH HOH . D 4 HOH A 241 541 419 HOH HOH . D 4 HOH A 242 542 522 HOH HOH . D 4 HOH A 243 543 489 HOH HOH . D 4 HOH A 244 544 470 HOH HOH . D 4 HOH A 245 545 476 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 O5' AR3 . . . B 2 15.625 2.59 28.968 1 24.65 ? O5' AR3 201 A 1 HETATM 2 C C5' AR3 . . . B 2 14.483 2.599 28.108 1 21.7 ? C5' AR3 201 A 1 HETATM 3 C C4' AR3 . . . B 2 14.681 3.515 26.861 1 18.06 ? C4' AR3 201 A 1 HETATM 4 O O4' AR3 . . . B 2 14.926 4.807 27.352 1 19.38 ? O4' AR3 201 A 1 HETATM 5 C C1' AR3 . . . B 2 15.684 5.598 26.403 1 20.31 ? C1' AR3 201 A 1 HETATM 6 N N1 AR3 . . . B 2 16.774 6.184 27.159 1 23.26 ? N1 AR3 201 A 1 HETATM 7 C C6 AR3 . . . B 2 17.44 5.481 28.129 1 24.27 ? C6 AR3 201 A 1 HETATM 8 C C5 AR3 . . . B 2 18.391 6.088 28.956 1 28.55 ? C5 AR3 201 A 1 HETATM 9 C C4 AR3 . . . B 2 18.706 7.473 28.704 1 30.13 ? C4 AR3 201 A 1 HETATM 10 N N3 AR3 . . . B 2 18.056 8.145 27.669 1 31.64 ? N3 AR3 201 A 1 HETATM 11 C C2 AR3 . . . B 2 17.071 7.55 26.929 1 25.25 ? C2 AR3 201 A 1 HETATM 12 O O2 AR3 . . . B 2 16.523 8.12 25.963 1 29.88 ? O2 AR3 201 A 1 HETATM 13 N N4 AR3 . . . B 2 19.657 8.093 29.422 1 44.49 ? N4 AR3 201 A 1 HETATM 14 C C2' AR3 . . . B 2 16.06 4.581 25.344 1 23.08 ? C2' AR3 201 A 1 HETATM 15 O O1 AR3 . . . B 2 17.41 4.867 24.908 1 27.11 ? O1 AR3 201 A 1 HETATM 16 C C3' AR3 . . . B 2 15.882 3.225 25.939 1 20.71 ? C3' AR3 201 A 1 HETATM 17 O O3' AR3 . . . B 2 15.544 2.185 24.948 1 27.15 ? O3' AR3 201 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 17 #