data_8J5E # _model_server_result.job_id 5jfk_q_IGUr4OfLvDhJFOA _model_server_result.datetime_utc '2024-10-10 14:19:10' _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 8j5e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 8J5E # _exptl.entry_id 8J5E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 259.282 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-azanyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)thiolan-2-yl]pyrimidin-2-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 90 _cell.entry_id 8J5E _cell.length_a 70.642 _cell.length_b 78.108 _cell.length_c 84.089 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8J5E _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall 'C 2c 2' _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 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 O4 S' _chem_comp.formula_weight 259.282 _chem_comp.id TQR _chem_comp.mon_nstd_flag . _chem_comp.name 4-azanyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)thiolan-2-yl]pyrimidin-2-one _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 C8 C9 TQR doub 293 n n C8 C7 TQR sing 294 n n N3 C7 TQR sing 295 n n C9 N1 TQR sing 296 n n C7 N2 TQR doub 297 n n C5 O3 TQR sing 298 n n C5 C1 TQR sing 299 n n N1 C6 TQR sing 300 n n N1 C4 TQR sing 301 n n N2 C6 TQR sing 302 n n C3 O2 TQR sing 303 n n C3 C4 TQR sing 304 n n C3 C2 TQR sing 305 n n C6 O4 TQR doub 306 n n C1 C2 TQR sing 307 n n C1 S1 TQR sing 308 n n C4 S1 TQR sing 309 n n C2 O1 TQR sing 310 n n N3 H1 TQR sing 311 n n N3 H2 TQR sing 312 n n C4 H3 TQR sing 313 n n C5 H4 TQR sing 314 n n C5 H5 TQR sing 315 n n C8 H6 TQR sing 316 n n C1 H7 TQR sing 317 n n C2 H8 TQR sing 318 n n C3 H9 TQR sing 319 n n C9 H10 TQR sing 320 n n O1 H11 TQR sing 321 n n O2 H12 TQR sing 322 n n O3 H13 TQR sing 323 n n # _atom_sites.entry_id 8J5E _atom_sites.fract_transf_matrix[1][1] 0.014156 _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] 0.012803 _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] 0.011892 _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 TQR A 1 301 1 TQR LIG . C 3 HOH A 1 401 107 HOH HOH . C 3 HOH A 2 402 249 HOH HOH . C 3 HOH A 3 403 155 HOH HOH . C 3 HOH A 4 404 81 HOH HOH . C 3 HOH A 5 405 96 HOH HOH . C 3 HOH A 6 406 122 HOH HOH . C 3 HOH A 7 407 176 HOH HOH . C 3 HOH A 8 408 232 HOH HOH . C 3 HOH A 9 409 259 HOH HOH . C 3 HOH A 10 410 272 HOH HOH . C 3 HOH A 11 411 71 HOH HOH . C 3 HOH A 12 412 83 HOH HOH . C 3 HOH A 13 413 26 HOH HOH . C 3 HOH A 14 414 89 HOH HOH . C 3 HOH A 15 415 140 HOH HOH . C 3 HOH A 16 416 36 HOH HOH . C 3 HOH A 17 417 217 HOH HOH . C 3 HOH A 18 418 29 HOH HOH . C 3 HOH A 19 419 221 HOH HOH . C 3 HOH A 20 420 172 HOH HOH . C 3 HOH A 21 421 80 HOH HOH . C 3 HOH A 22 422 25 HOH HOH . C 3 HOH A 23 423 238 HOH HOH . C 3 HOH A 24 424 220 HOH HOH . C 3 HOH A 25 425 269 HOH HOH . C 3 HOH A 26 426 87 HOH HOH . C 3 HOH A 27 427 241 HOH HOH . C 3 HOH A 28 428 263 HOH HOH . C 3 HOH A 29 429 5 HOH HOH . C 3 HOH A 30 430 24 HOH HOH . C 3 HOH A 31 431 196 HOH HOH . C 3 HOH A 32 432 7 HOH HOH . C 3 HOH A 33 433 2 HOH HOH . C 3 HOH A 34 434 195 HOH HOH . C 3 HOH A 35 435 105 HOH HOH . C 3 HOH A 36 436 200 HOH HOH . C 3 HOH A 37 437 133 HOH HOH . C 3 HOH A 38 438 78 HOH HOH . C 3 HOH A 39 439 4 HOH HOH . C 3 HOH A 40 440 69 HOH HOH . C 3 HOH A 41 441 160 HOH HOH . C 3 HOH A 42 442 9 HOH HOH . C 3 HOH A 43 443 253 HOH HOH . C 3 HOH A 44 444 129 HOH HOH . C 3 HOH A 45 445 177 HOH HOH . C 3 HOH A 46 446 90 HOH HOH . C 3 HOH A 47 447 23 HOH HOH . C 3 HOH A 48 448 180 HOH HOH . C 3 HOH A 49 449 181 HOH HOH . C 3 HOH A 50 450 169 HOH HOH . C 3 HOH A 51 451 281 HOH HOH . C 3 HOH A 52 452 109 HOH HOH . C 3 HOH A 53 453 95 HOH HOH . C 3 HOH A 54 454 3 HOH HOH . C 3 HOH A 55 455 77 HOH HOH . C 3 HOH A 56 456 21 HOH HOH . C 3 HOH A 57 457 10 HOH HOH . C 3 HOH A 58 458 275 HOH HOH . C 3 HOH A 59 459 40 HOH HOH . C 3 HOH A 60 460 76 HOH HOH . C 3 HOH A 61 461 60 HOH HOH . C 3 HOH A 62 462 37 HOH HOH . C 3 HOH A 63 463 59 HOH HOH . C 3 HOH A 64 464 186 HOH HOH . C 3 HOH A 65 465 203 HOH HOH . C 3 HOH A 66 466 282 HOH HOH . C 3 HOH A 67 467 273 HOH HOH . C 3 HOH A 68 468 43 HOH HOH . C 3 HOH A 69 469 125 HOH HOH . C 3 HOH A 70 470 19 HOH HOH . C 3 HOH A 71 471 11 HOH HOH . C 3 HOH A 72 472 131 HOH HOH . C 3 HOH A 73 473 33 HOH HOH . C 3 HOH A 74 474 31 HOH HOH . C 3 HOH A 75 475 101 HOH HOH . C 3 HOH A 76 476 86 HOH HOH . C 3 HOH A 77 477 53 HOH HOH . C 3 HOH A 78 478 28 HOH HOH . C 3 HOH A 79 479 93 HOH HOH . C 3 HOH A 80 480 18 HOH HOH . C 3 HOH A 81 481 139 HOH HOH . C 3 HOH A 82 482 30 HOH HOH . C 3 HOH A 83 483 14 HOH HOH . C 3 HOH A 84 484 39 HOH HOH . C 3 HOH A 85 485 98 HOH HOH . C 3 HOH A 86 486 222 HOH HOH . C 3 HOH A 87 487 8 HOH HOH . C 3 HOH A 88 488 13 HOH HOH . C 3 HOH A 89 489 17 HOH HOH . C 3 HOH A 90 490 16 HOH HOH . C 3 HOH A 91 491 35 HOH HOH . C 3 HOH A 92 492 22 HOH HOH . C 3 HOH A 93 493 6 HOH HOH . C 3 HOH A 94 494 42 HOH HOH . C 3 HOH A 95 495 100 HOH HOH . C 3 HOH A 96 496 82 HOH HOH . C 3 HOH A 97 497 143 HOH HOH . C 3 HOH A 98 498 20 HOH HOH . C 3 HOH A 99 499 197 HOH HOH . C 3 HOH A 100 500 150 HOH HOH . C 3 HOH A 101 501 38 HOH HOH . C 3 HOH A 102 502 55 HOH HOH . C 3 HOH A 103 503 120 HOH HOH . C 3 HOH A 104 504 110 HOH HOH . C 3 HOH A 105 505 94 HOH HOH . C 3 HOH A 106 506 215 HOH HOH . C 3 HOH A 107 507 34 HOH HOH . C 3 HOH A 108 508 124 HOH HOH . C 3 HOH A 109 509 72 HOH HOH . C 3 HOH A 110 510 1 HOH HOH . C 3 HOH A 111 511 88 HOH HOH . C 3 HOH A 112 512 45 HOH HOH . C 3 HOH A 113 513 113 HOH HOH . C 3 HOH A 114 514 65 HOH HOH . C 3 HOH A 115 515 67 HOH HOH . C 3 HOH A 116 516 145 HOH HOH . C 3 HOH A 117 517 255 HOH HOH . C 3 HOH A 118 518 68 HOH HOH . C 3 HOH A 119 519 118 HOH HOH . C 3 HOH A 120 520 108 HOH HOH . C 3 HOH A 121 521 187 HOH HOH . C 3 HOH A 122 522 132 HOH HOH . C 3 HOH A 123 523 179 HOH HOH . C 3 HOH A 124 524 64 HOH HOH . C 3 HOH A 125 525 27 HOH HOH . C 3 HOH A 126 526 144 HOH HOH . C 3 HOH A 127 527 227 HOH HOH . C 3 HOH A 128 528 46 HOH HOH . C 3 HOH A 129 529 74 HOH HOH . C 3 HOH A 130 530 97 HOH HOH . C 3 HOH A 131 531 141 HOH HOH . C 3 HOH A 132 532 52 HOH HOH . C 3 HOH A 133 533 199 HOH HOH . C 3 HOH A 134 534 224 HOH HOH . C 3 HOH A 135 535 152 HOH HOH . C 3 HOH A 136 536 84 HOH HOH . C 3 HOH A 137 537 243 HOH HOH . C 3 HOH A 138 538 157 HOH HOH . C 3 HOH A 139 539 198 HOH HOH . C 3 HOH A 140 540 15 HOH HOH . C 3 HOH A 141 541 12 HOH HOH . C 3 HOH A 142 542 63 HOH HOH . C 3 HOH A 143 543 54 HOH HOH . C 3 HOH A 144 544 114 HOH HOH . C 3 HOH A 145 545 112 HOH HOH . C 3 HOH A 146 546 102 HOH HOH . C 3 HOH A 147 547 51 HOH HOH . C 3 HOH A 148 548 75 HOH HOH . C 3 HOH A 149 549 32 HOH HOH . C 3 HOH A 150 550 130 HOH HOH . C 3 HOH A 151 551 57 HOH HOH . C 3 HOH A 152 552 103 HOH HOH . C 3 HOH A 153 553 182 HOH HOH . C 3 HOH A 154 554 159 HOH HOH . C 3 HOH A 155 555 146 HOH HOH . C 3 HOH A 156 556 151 HOH HOH . C 3 HOH A 157 557 270 HOH HOH . C 3 HOH A 158 558 126 HOH HOH . C 3 HOH A 159 559 257 HOH HOH . C 3 HOH A 160 560 73 HOH HOH . C 3 HOH A 161 561 166 HOH HOH . C 3 HOH A 162 562 226 HOH HOH . C 3 HOH A 163 563 50 HOH HOH . C 3 HOH A 164 564 137 HOH HOH . C 3 HOH A 165 565 117 HOH HOH . C 3 HOH A 166 566 56 HOH HOH . C 3 HOH A 167 567 47 HOH HOH . C 3 HOH A 168 568 44 HOH HOH . C 3 HOH A 169 569 70 HOH HOH . C 3 HOH A 170 570 266 HOH HOH . C 3 HOH A 171 571 106 HOH HOH . C 3 HOH A 172 572 230 HOH HOH . C 3 HOH A 173 573 66 HOH HOH . C 3 HOH A 174 574 280 HOH HOH . C 3 HOH A 175 575 237 HOH HOH . C 3 HOH A 176 576 136 HOH HOH . C 3 HOH A 177 577 161 HOH HOH . C 3 HOH A 178 578 116 HOH HOH . C 3 HOH A 179 579 171 HOH HOH . C 3 HOH A 180 580 104 HOH HOH . C 3 HOH A 181 581 261 HOH HOH . C 3 HOH A 182 582 268 HOH HOH . C 3 HOH A 183 583 208 HOH HOH . C 3 HOH A 184 584 251 HOH HOH . C 3 HOH A 185 585 115 HOH HOH . C 3 HOH A 186 586 127 HOH HOH . C 3 HOH A 187 587 264 HOH HOH . C 3 HOH A 188 588 148 HOH HOH . C 3 HOH A 189 589 185 HOH HOH . C 3 HOH A 190 590 229 HOH HOH . C 3 HOH A 191 591 142 HOH HOH . C 3 HOH A 192 592 128 HOH HOH . C 3 HOH A 193 593 48 HOH HOH . C 3 HOH A 194 594 225 HOH HOH . C 3 HOH A 195 595 240 HOH HOH . C 3 HOH A 196 596 260 HOH HOH . C 3 HOH A 197 597 183 HOH HOH . C 3 HOH A 198 598 244 HOH HOH . C 3 HOH A 199 599 207 HOH HOH . C 3 HOH A 200 600 231 HOH HOH . C 3 HOH A 201 601 184 HOH HOH . C 3 HOH A 202 602 162 HOH HOH . C 3 HOH A 203 603 163 HOH HOH . C 3 HOH A 204 604 173 HOH HOH . C 3 HOH A 205 605 214 HOH HOH . C 3 HOH A 206 606 279 HOH HOH . C 3 HOH A 207 607 91 HOH HOH . C 3 HOH A 208 608 188 HOH HOH . C 3 HOH A 209 609 164 HOH HOH . C 3 HOH A 210 610 242 HOH HOH . C 3 HOH A 211 611 174 HOH HOH . C 3 HOH A 212 612 79 HOH HOH . C 3 HOH A 213 613 190 HOH HOH . C 3 HOH A 214 614 138 HOH HOH . C 3 HOH A 215 615 262 HOH HOH . C 3 HOH A 216 616 167 HOH HOH . C 3 HOH A 217 617 62 HOH HOH . C 3 HOH A 218 618 252 HOH HOH . C 3 HOH A 219 619 175 HOH HOH . C 3 HOH A 220 620 210 HOH HOH . C 3 HOH A 221 621 223 HOH HOH . C 3 HOH A 222 622 193 HOH HOH . C 3 HOH A 223 623 234 HOH HOH . C 3 HOH A 224 624 194 HOH HOH . C 3 HOH A 225 625 119 HOH HOH . C 3 HOH A 226 626 178 HOH HOH . C 3 HOH A 227 627 201 HOH HOH . C 3 HOH A 228 628 278 HOH HOH . C 3 HOH A 229 629 154 HOH HOH . C 3 HOH A 230 630 135 HOH HOH . C 3 HOH A 231 631 149 HOH HOH . C 3 HOH A 232 632 245 HOH HOH . C 3 HOH A 233 633 92 HOH HOH . C 3 HOH A 234 634 61 HOH HOH . C 3 HOH A 235 635 99 HOH HOH . C 3 HOH A 236 636 211 HOH HOH . C 3 HOH A 237 637 58 HOH HOH . C 3 HOH A 238 638 276 HOH HOH . C 3 HOH A 239 639 235 HOH HOH . C 3 HOH A 240 640 111 HOH HOH . C 3 HOH A 241 641 123 HOH HOH . C 3 HOH A 242 642 209 HOH HOH . C 3 HOH A 243 643 191 HOH HOH . C 3 HOH A 244 644 165 HOH HOH . C 3 HOH A 245 645 121 HOH HOH . C 3 HOH A 246 646 147 HOH HOH . C 3 HOH A 247 647 265 HOH HOH . C 3 HOH A 248 648 49 HOH HOH . C 3 HOH A 249 649 85 HOH HOH . C 3 HOH A 250 650 246 HOH HOH . C 3 HOH A 251 651 219 HOH HOH . C 3 HOH A 252 652 216 HOH HOH . C 3 HOH A 253 653 250 HOH HOH . C 3 HOH A 254 654 158 HOH HOH . C 3 HOH A 255 655 258 HOH HOH . C 3 HOH A 256 656 256 HOH HOH . C 3 HOH A 257 657 134 HOH HOH . C 3 HOH A 258 658 189 HOH HOH . C 3 HOH A 259 659 254 HOH HOH . C 3 HOH A 260 660 248 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 TQR . . . B 2 16.181 14.044 2.625 1 12.96 ? N1 TQR 301 A 1 HETATM 2 N N3 TQR . . . B 2 19.255 11.912 0.749 1 11.5 ? N3 TQR 301 A 1 HETATM 3 C C4 TQR . . . B 2 15.152 14.769 3.379 1 13.38 ? C4 TQR 301 A 1 HETATM 4 C C5 TQR . . . B 2 11.798 15.066 2.016 1 32.31 ? C5 TQR 301 A 1 HETATM 5 C C6 TQR . . . B 2 17.172 13.495 3.297 1 11.67 ? C6 TQR 301 A 1 HETATM 6 C C7 TQR . . . B 2 18.176 12.667 1.341 1 13.74 ? C7 TQR 301 A 1 HETATM 7 C C8 TQR . . . B 2 17.057 13.277 0.51 1 11.63 ? C8 TQR 301 A 1 HETATM 8 C C1 TQR . . . B 2 12.536 15.108 3.359 1 24.6 ? C1 TQR 301 A 1 HETATM 9 C C2 TQR . . . B 2 13.351 16.39 3.441 1 20.93 ? C2 TQR 301 A 1 HETATM 10 C C3 TQR . . . B 2 14.693 16.092 2.753 1 14.83 ? C3 TQR 301 A 1 HETATM 11 C C9 TQR . . . B 2 16.122 13.948 1.3 1 14.89 ? C9 TQR 301 A 1 HETATM 12 N N2 TQR . . . B 2 18.239 12.769 2.748 1 10.81 ? N2 TQR 301 A 1 HETATM 13 O O1 TQR . . . B 2 13.578 16.669 4.789 1 17.71 ? O1 TQR 301 A 1 HETATM 14 O O2 TQR . . . B 2 15.573 17.123 3.048 1 17.53 ? O2 TQR 301 A 1 HETATM 15 O O3 TQR . . . B 2 10.437 15.291 2.245 1 36.51 ? O3 TQR 301 A 1 HETATM 16 O O4 TQR . . . B 2 17.218 13.607 4.658 1 11.62 ? O4 TQR 301 A 1 HETATM 17 S S1 TQR . . . B 2 13.681 13.72 3.457 1 25.67 ? S1 TQR 301 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 17 #