data_8OJK # _model_server_result.job_id xSXGsFpVyN0c4c43SC28kg _model_server_result.datetime_utc '2024-10-20 00:43:43' _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 8ojk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 8OJK # _exptl.entry_id 8OJK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 191.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxane-2-carboxamide _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 8OJK _cell.length_a 36.09 _cell.length_b 57.66 _cell.length_c 61.8 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8OJK _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 B S1 YIO . A YIO 301 1_555 C C2' VPL . A VPL 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.84 ? metalc ? metalc1 D MG MG . A MG 303 1_555 E O HOH . A HOH 460 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? # _chem_comp.formula 'C7 H13 N O5' _chem_comp.formula_weight 191.182 _chem_comp.id VPL _chem_comp.mon_nstd_flag . _chem_comp.name (2~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxane-2-carboxamide _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 O3' C3' VPL sing 376 n n O4' C4' VPL sing 377 n n C3' C4' VPL sing 378 n n C3' C2' VPL sing 379 n n C4' C5' VPL sing 380 n n C2' C1' VPL sing 381 n n C5' C6' VPL sing 382 n n C5' O5' VPL sing 383 n n C6' O6' VPL sing 384 n n O5' C1' VPL sing 385 n n C1' C7 VPL sing 386 n n C7 N1 VPL sing 387 n n C7 O7 VPL doub 388 n n C5' H1 VPL sing 389 n n C4' H2 VPL sing 390 n n C3' H3 VPL sing 391 n n C2' H4 VPL sing 392 n n C2' H5 VPL sing 393 n n C1' H6 VPL sing 394 n n C6' H7 VPL sing 395 n n C6' H8 VPL sing 396 n n O6' H9 VPL sing 397 n n O4' H10 VPL sing 398 n n O3' H11 VPL sing 399 n n N1 H12 VPL sing 400 n n N1 H13 VPL sing 401 n n # _atom_sites.entry_id 8OJK _atom_sites.fract_transf_matrix[1][1] 0.027709 _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] 0.017343 _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] 0.016181 _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 YIO A 1 301 301 YIO YIO . C 3 VPL A 1 302 302 VPL LLB . D 4 MG A 1 303 1 MG MG . E 5 HOH A 1 401 219 HOH HOH . E 5 HOH A 2 402 195 HOH HOH . E 5 HOH A 3 403 90 HOH HOH . E 5 HOH A 4 404 222 HOH HOH . E 5 HOH A 5 405 51 HOH HOH . E 5 HOH A 6 406 130 HOH HOH . E 5 HOH A 7 407 161 HOH HOH . E 5 HOH A 8 408 209 HOH HOH . E 5 HOH A 9 409 6 HOH HOH . E 5 HOH A 10 410 59 HOH HOH . E 5 HOH A 11 411 64 HOH HOH . E 5 HOH A 12 412 184 HOH HOH . E 5 HOH A 13 413 28 HOH HOH . E 5 HOH A 14 414 58 HOH HOH . E 5 HOH A 15 415 146 HOH HOH . E 5 HOH A 16 416 193 HOH HOH . E 5 HOH A 17 417 126 HOH HOH . E 5 HOH A 18 418 187 HOH HOH . E 5 HOH A 19 419 3 HOH HOH . E 5 HOH A 20 420 233 HOH HOH . E 5 HOH A 21 421 189 HOH HOH . E 5 HOH A 22 422 34 HOH HOH . E 5 HOH A 23 423 203 HOH HOH . E 5 HOH A 24 424 194 HOH HOH . E 5 HOH A 25 425 36 HOH HOH . E 5 HOH A 26 426 73 HOH HOH . E 5 HOH A 27 427 10 HOH HOH . E 5 HOH A 28 428 145 HOH HOH . E 5 HOH A 29 429 111 HOH HOH . E 5 HOH A 30 430 167 HOH HOH . E 5 HOH A 31 431 16 HOH HOH . E 5 HOH A 32 432 123 HOH HOH . E 5 HOH A 33 433 42 HOH HOH . E 5 HOH A 34 434 232 HOH HOH . E 5 HOH A 35 435 142 HOH HOH . E 5 HOH A 36 436 196 HOH HOH . E 5 HOH A 37 437 15 HOH HOH . E 5 HOH A 38 438 231 HOH HOH . E 5 HOH A 39 439 106 HOH HOH . E 5 HOH A 40 440 92 HOH HOH . E 5 HOH A 41 441 212 HOH HOH . E 5 HOH A 42 442 127 HOH HOH . E 5 HOH A 43 443 71 HOH HOH . E 5 HOH A 44 444 103 HOH HOH . E 5 HOH A 45 445 41 HOH HOH . E 5 HOH A 46 446 107 HOH HOH . E 5 HOH A 47 447 119 HOH HOH . E 5 HOH A 48 448 12 HOH HOH . E 5 HOH A 49 449 57 HOH HOH . E 5 HOH A 50 450 113 HOH HOH . E 5 HOH A 51 451 17 HOH HOH . E 5 HOH A 52 452 158 HOH HOH . E 5 HOH A 53 453 238 HOH HOH . E 5 HOH A 54 454 32 HOH HOH . E 5 HOH A 55 455 70 HOH HOH . E 5 HOH A 56 456 135 HOH HOH . E 5 HOH A 57 457 131 HOH HOH . E 5 HOH A 58 458 102 HOH HOH . E 5 HOH A 59 459 114 HOH HOH . E 5 HOH A 60 460 82 HOH HOH . E 5 HOH A 61 461 86 HOH HOH . E 5 HOH A 62 462 122 HOH HOH . E 5 HOH A 63 463 164 HOH HOH . E 5 HOH A 64 464 18 HOH HOH . E 5 HOH A 65 465 150 HOH HOH . E 5 HOH A 66 466 69 HOH HOH . E 5 HOH A 67 467 214 HOH HOH . E 5 HOH A 68 468 91 HOH HOH . E 5 HOH A 69 469 141 HOH HOH . E 5 HOH A 70 470 207 HOH HOH . E 5 HOH A 71 471 46 HOH HOH . E 5 HOH A 72 472 88 HOH HOH . E 5 HOH A 73 473 49 HOH HOH . E 5 HOH A 74 474 163 HOH HOH . E 5 HOH A 75 475 63 HOH HOH . E 5 HOH A 76 476 105 HOH HOH . E 5 HOH A 77 477 44 HOH HOH . E 5 HOH A 78 478 97 HOH HOH . E 5 HOH A 79 479 132 HOH HOH . E 5 HOH A 80 480 72 HOH HOH . E 5 HOH A 81 481 154 HOH HOH . E 5 HOH A 82 482 178 HOH HOH . E 5 HOH A 83 483 39 HOH HOH . E 5 HOH A 84 484 4 HOH HOH . E 5 HOH A 85 485 65 HOH HOH . E 5 HOH A 86 486 247 HOH HOH . E 5 HOH A 87 487 197 HOH HOH . E 5 HOH A 88 488 30 HOH HOH . E 5 HOH A 89 489 43 HOH HOH . E 5 HOH A 90 490 165 HOH HOH . E 5 HOH A 91 491 68 HOH HOH . E 5 HOH A 92 492 237 HOH HOH . E 5 HOH A 93 493 147 HOH HOH . E 5 HOH A 94 494 50 HOH HOH . E 5 HOH A 95 495 22 HOH HOH . E 5 HOH A 96 496 162 HOH HOH . E 5 HOH A 97 497 54 HOH HOH . E 5 HOH A 98 498 239 HOH HOH . E 5 HOH A 99 499 211 HOH HOH . E 5 HOH A 100 500 94 HOH HOH . E 5 HOH A 101 501 87 HOH HOH . E 5 HOH A 102 502 8 HOH HOH . E 5 HOH A 103 503 89 HOH HOH . E 5 HOH A 104 504 31 HOH HOH . E 5 HOH A 105 505 166 HOH HOH . E 5 HOH A 106 506 133 HOH HOH . E 5 HOH A 107 507 120 HOH HOH . E 5 HOH A 108 508 29 HOH HOH . E 5 HOH A 109 509 38 HOH HOH . E 5 HOH A 110 510 98 HOH HOH . E 5 HOH A 111 511 45 HOH HOH . E 5 HOH A 112 512 55 HOH HOH . E 5 HOH A 113 513 104 HOH HOH . E 5 HOH A 114 514 21 HOH HOH . E 5 HOH A 115 515 149 HOH HOH . E 5 HOH A 116 516 129 HOH HOH . E 5 HOH A 117 517 183 HOH HOH . E 5 HOH A 118 518 153 HOH HOH . E 5 HOH A 119 519 160 HOH HOH . E 5 HOH A 120 520 25 HOH HOH . E 5 HOH A 121 521 56 HOH HOH . E 5 HOH A 122 522 84 HOH HOH . E 5 HOH A 123 523 117 HOH HOH . E 5 HOH A 124 524 27 HOH HOH . E 5 HOH A 125 525 151 HOH HOH . E 5 HOH A 126 526 85 HOH HOH . E 5 HOH A 127 527 47 HOH HOH . E 5 HOH A 128 528 206 HOH HOH . E 5 HOH A 129 529 37 HOH HOH . E 5 HOH A 130 530 112 HOH HOH . E 5 HOH A 131 531 83 HOH HOH . E 5 HOH A 132 532 148 HOH HOH . E 5 HOH A 133 533 236 HOH HOH . E 5 HOH A 134 534 78 HOH HOH . E 5 HOH A 135 535 9 HOH HOH . E 5 HOH A 136 536 110 HOH HOH . E 5 HOH A 137 537 174 HOH HOH . E 5 HOH A 138 538 96 HOH HOH . E 5 HOH A 139 539 116 HOH HOH . E 5 HOH A 140 540 121 HOH HOH . E 5 HOH A 141 541 7 HOH HOH . E 5 HOH A 142 542 53 HOH HOH . E 5 HOH A 143 543 95 HOH HOH . E 5 HOH A 144 544 204 HOH HOH . E 5 HOH A 145 545 128 HOH HOH . E 5 HOH A 146 546 23 HOH HOH . E 5 HOH A 147 547 199 HOH HOH . E 5 HOH A 148 548 186 HOH HOH . E 5 HOH A 149 549 33 HOH HOH . E 5 HOH A 150 550 13 HOH HOH . E 5 HOH A 151 551 198 HOH HOH . E 5 HOH A 152 552 5 HOH HOH . E 5 HOH A 153 553 48 HOH HOH . E 5 HOH A 154 554 40 HOH HOH . E 5 HOH A 155 555 172 HOH HOH . E 5 HOH A 156 556 188 HOH HOH . E 5 HOH A 157 557 66 HOH HOH . E 5 HOH A 158 558 19 HOH HOH . E 5 HOH A 159 559 173 HOH HOH . E 5 HOH A 160 560 52 HOH HOH . E 5 HOH A 161 561 124 HOH HOH . E 5 HOH A 162 562 26 HOH HOH . E 5 HOH A 163 563 244 HOH HOH . E 5 HOH A 164 564 109 HOH HOH . E 5 HOH A 165 565 11 HOH HOH . E 5 HOH A 166 566 230 HOH HOH . E 5 HOH A 167 567 179 HOH HOH . E 5 HOH A 168 568 152 HOH HOH . E 5 HOH A 169 569 1 HOH HOH . E 5 HOH A 170 570 208 HOH HOH . E 5 HOH A 171 571 140 HOH HOH . E 5 HOH A 172 572 168 HOH HOH . E 5 HOH A 173 573 205 HOH HOH . E 5 HOH A 174 574 218 HOH HOH . E 5 HOH A 175 575 80 HOH HOH . E 5 HOH A 176 576 200 HOH HOH . E 5 HOH A 177 577 35 HOH HOH . E 5 HOH A 178 578 175 HOH HOH . E 5 HOH A 179 579 125 HOH HOH . E 5 HOH A 180 580 137 HOH HOH . E 5 HOH A 181 581 246 HOH HOH . E 5 HOH A 182 582 182 HOH HOH . E 5 HOH A 183 583 191 HOH HOH . E 5 HOH A 184 584 241 HOH HOH . E 5 HOH A 185 585 76 HOH HOH . E 5 HOH A 186 586 192 HOH HOH . E 5 HOH A 187 587 242 HOH HOH . E 5 HOH A 188 588 229 HOH HOH . E 5 HOH A 189 589 235 HOH HOH . E 5 HOH A 190 590 2 HOH HOH . E 5 HOH A 191 591 170 HOH HOH . E 5 HOH A 192 592 171 HOH HOH . E 5 HOH A 193 593 177 HOH HOH . E 5 HOH A 194 594 118 HOH HOH . E 5 HOH A 195 595 100 HOH HOH . E 5 HOH A 196 596 155 HOH HOH . E 5 HOH A 197 597 20 HOH HOH . E 5 HOH A 198 598 248 HOH HOH . E 5 HOH A 199 599 169 HOH HOH . E 5 HOH A 200 600 190 HOH HOH . E 5 HOH A 201 601 139 HOH HOH . E 5 HOH A 202 602 115 HOH HOH . E 5 HOH A 203 603 24 HOH HOH . E 5 HOH A 204 604 216 HOH HOH . E 5 HOH A 205 605 108 HOH HOH . E 5 HOH A 206 606 61 HOH HOH . E 5 HOH A 207 607 79 HOH HOH . E 5 HOH A 208 608 202 HOH HOH . E 5 HOH A 209 609 134 HOH HOH . E 5 HOH A 210 610 185 HOH HOH . E 5 HOH A 211 611 144 HOH HOH . E 5 HOH A 212 612 99 HOH HOH . E 5 HOH A 213 613 225 HOH HOH . E 5 HOH A 214 614 226 HOH HOH . E 5 HOH A 215 615 217 HOH HOH . E 5 HOH A 216 616 221 HOH HOH . E 5 HOH A 217 617 81 HOH HOH . E 5 HOH A 218 618 93 HOH HOH . E 5 HOH A 219 619 234 HOH HOH . E 5 HOH A 220 620 159 HOH HOH . E 5 HOH A 221 621 210 HOH HOH . E 5 HOH A 222 622 228 HOH HOH . E 5 HOH A 223 623 138 HOH HOH . E 5 HOH A 224 624 220 HOH HOH . E 5 HOH A 225 625 223 HOH HOH . E 5 HOH A 226 626 14 HOH HOH . E 5 HOH A 227 627 77 HOH HOH . E 5 HOH A 228 628 75 HOH HOH . E 5 HOH A 229 629 245 HOH HOH . E 5 HOH A 230 630 60 HOH HOH . E 5 HOH A 231 631 157 HOH HOH . E 5 HOH A 232 632 136 HOH HOH . E 5 HOH A 233 633 176 HOH HOH . E 5 HOH A 234 634 74 HOH HOH . E 5 HOH A 235 635 240 HOH HOH . E 5 HOH A 236 636 67 HOH HOH . E 5 HOH A 237 637 181 HOH HOH . E 5 HOH A 238 638 62 HOH HOH . E 5 HOH A 239 639 201 HOH HOH . E 5 HOH A 240 640 143 HOH HOH . E 5 HOH A 241 641 180 HOH HOH . E 5 HOH A 242 642 101 HOH HOH . E 5 HOH A 243 643 227 HOH HOH . E 5 HOH A 244 644 224 HOH HOH . E 5 HOH A 245 645 156 HOH HOH . E 5 HOH A 246 646 243 HOH HOH . E 5 HOH A 247 647 215 HOH HOH . E 5 HOH A 248 648 213 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 C C7 VPL . . . C 3 22.884 38.573 34.998 1 20.54 ? C7 VPL 302 A 1 HETATM 2 C C5' VPL . . . C 3 24.957 40.529 32.682 1 18.73 ? C5' VPL 302 A 1 HETATM 3 C C4' VPL . . . C 3 24.303 40.255 31.31 1 16.84 ? C4' VPL 302 A 1 HETATM 4 C C3' VPL . . . C 3 23.833 38.804 31.267 1 17.57 ? C3' VPL 302 A 1 HETATM 5 C C2' VPL . . . C 3 22.942 38.453 32.464 1 17.16 ? C2' VPL 302 A 1 HETATM 6 C C1' VPL . . . C 3 23.689 38.829 33.751 1 18.55 ? C1' VPL 302 A 1 HETATM 7 O O5' VPL . . . C 3 23.999 40.223 33.706 1 18.87 ? O5' VPL 302 A 1 HETATM 8 C C6' VPL . . . C 3 25.394 41.964 32.899 1 19.48 ? C6' VPL 302 A 1 HETATM 9 O O6' VPL . . . C 3 26.29 42.017 34.025 1 22.08 ? O6' VPL 302 A 1 HETATM 10 O O4' VPL . . . C 3 23.152 41.057 31.102 1 16.31 ? O4' VPL 302 A 1 HETATM 11 O O3' VPL . . . C 3 23.121 38.535 30.07 1 14.33 ? O3' VPL 302 A 1 HETATM 12 N N1 VPL . . . C 3 22.609 37.179 35.306 1 18.21 ? N1 VPL 302 A 1 HETATM 13 O O7 VPL . . . C 3 22.449 39.439 35.73 1 24.12 ? O7 VPL 302 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 13 #