data_8OJI # _model_server_result.job_id S58pdTnXJvM0UNdFV_sNTw _model_server_result.datetime_utc '2024-12-29 14:37:15' _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 8oji # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":304}' # _entry.id 8OJI # _exptl.entry_id 8OJI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 206.193 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'methyl (2~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxane-2-carboxylate' _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 8OJI _cell.length_a 35.94 _cell.length_b 57.87 _cell.length_c 62.65 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8OJI _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,F _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 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id D _struct_conn.ptnr1_label_atom_id S1 _struct_conn.ptnr1_label_comp_id YIO _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id YIO _struct_conn.ptnr1_auth_seq_id 303 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id C2' _struct_conn.ptnr2_label_comp_id VPH _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id VPH _struct_conn.ptnr2_auth_seq_id 304 _struct_conn.ptnr2_symmetry 1_555 _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 1.827 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C8 H14 O6' _chem_comp.formula_weight 206.193 _chem_comp.id VPH _chem_comp.mon_nstd_flag . _chem_comp.name 'methyl (2~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxane-2-carboxylate' _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' VPH sing 376 n n O4' C4' VPH sing 377 n n C3' C4' VPH sing 378 n n C3' C2' VPH sing 379 n n C4' C5' VPH sing 380 n n C2' C1' VPH sing 381 n n C5' C6' VPH sing 382 n n C5' O5' VPH sing 383 n n C6' O6' VPH sing 384 n n O5' C1' VPH sing 385 n n C1' C7 VPH sing 386 n n C7 O7 VPH doub 387 n n C7 O8 VPH sing 388 n n O8 C9 VPH sing 389 n n C5' H1 VPH sing 390 n n C4' H2 VPH sing 391 n n C3' H3 VPH sing 392 n n C2' H4 VPH sing 393 n n C2' H5 VPH sing 394 n n C1' H6 VPH sing 395 n n C6' H7 VPH sing 396 n n C6' H8 VPH sing 397 n n O6' H9 VPH sing 398 n n O4' H10 VPH sing 399 n n O3' H11 VPH sing 400 n n C9 H12 VPH sing 401 n n C9 H13 VPH sing 402 n n C9 H14 VPH sing 403 n n # _atom_sites.entry_id 8OJI _atom_sites.fract_transf_matrix[1][1] 0.027824 _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] 0.01728 _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] 0.015962 _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 CL A 1 301 1 CL CL . C 2 CL A 1 302 2 CL CL . D 3 YIO A 1 303 301 YIO YIO . E 4 VPH A 1 304 302 VPH LLA . F 5 HOH A 1 401 99 HOH HOH . F 5 HOH A 2 402 214 HOH HOH . F 5 HOH A 3 403 88 HOH HOH . F 5 HOH A 4 404 223 HOH HOH . F 5 HOH A 5 405 187 HOH HOH . F 5 HOH A 6 406 234 HOH HOH . F 5 HOH A 7 407 190 HOH HOH . F 5 HOH A 8 408 11 HOH HOH . F 5 HOH A 9 409 167 HOH HOH . F 5 HOH A 10 410 128 HOH HOH . F 5 HOH A 11 411 155 HOH HOH . F 5 HOH A 12 412 106 HOH HOH . F 5 HOH A 13 413 81 HOH HOH . F 5 HOH A 14 414 21 HOH HOH . F 5 HOH A 15 415 211 HOH HOH . F 5 HOH A 16 416 95 HOH HOH . F 5 HOH A 17 417 195 HOH HOH . F 5 HOH A 18 418 34 HOH HOH . F 5 HOH A 19 419 14 HOH HOH . F 5 HOH A 20 420 145 HOH HOH . F 5 HOH A 21 421 204 HOH HOH . F 5 HOH A 22 422 168 HOH HOH . F 5 HOH A 23 423 117 HOH HOH . F 5 HOH A 24 424 49 HOH HOH . F 5 HOH A 25 425 169 HOH HOH . F 5 HOH A 26 426 80 HOH HOH . F 5 HOH A 27 427 161 HOH HOH . F 5 HOH A 28 428 25 HOH HOH . F 5 HOH A 29 429 8 HOH HOH . F 5 HOH A 30 430 102 HOH HOH . F 5 HOH A 31 431 115 HOH HOH . F 5 HOH A 32 432 186 HOH HOH . F 5 HOH A 33 433 164 HOH HOH . F 5 HOH A 34 434 89 HOH HOH . F 5 HOH A 35 435 9 HOH HOH . F 5 HOH A 36 436 78 HOH HOH . F 5 HOH A 37 437 53 HOH HOH . F 5 HOH A 38 438 210 HOH HOH . F 5 HOH A 39 439 194 HOH HOH . F 5 HOH A 40 440 132 HOH HOH . F 5 HOH A 41 441 103 HOH HOH . F 5 HOH A 42 442 230 HOH HOH . F 5 HOH A 43 443 86 HOH HOH . F 5 HOH A 44 444 55 HOH HOH . F 5 HOH A 45 445 68 HOH HOH . F 5 HOH A 46 446 29 HOH HOH . F 5 HOH A 47 447 98 HOH HOH . F 5 HOH A 48 448 56 HOH HOH . F 5 HOH A 49 449 4 HOH HOH . F 5 HOH A 50 450 142 HOH HOH . F 5 HOH A 51 451 13 HOH HOH . F 5 HOH A 52 452 10 HOH HOH . F 5 HOH A 53 453 209 HOH HOH . F 5 HOH A 54 454 146 HOH HOH . F 5 HOH A 55 455 108 HOH HOH . F 5 HOH A 56 456 232 HOH HOH . F 5 HOH A 57 457 123 HOH HOH . F 5 HOH A 58 458 84 HOH HOH . F 5 HOH A 59 459 62 HOH HOH . F 5 HOH A 60 460 32 HOH HOH . F 5 HOH A 61 461 185 HOH HOH . F 5 HOH A 62 462 150 HOH HOH . F 5 HOH A 63 463 101 HOH HOH . F 5 HOH A 64 464 151 HOH HOH . F 5 HOH A 65 465 5 HOH HOH . F 5 HOH A 66 466 97 HOH HOH . F 5 HOH A 67 467 147 HOH HOH . F 5 HOH A 68 468 119 HOH HOH . F 5 HOH A 69 469 39 HOH HOH . F 5 HOH A 70 470 38 HOH HOH . F 5 HOH A 71 471 41 HOH HOH . F 5 HOH A 72 472 70 HOH HOH . F 5 HOH A 73 473 17 HOH HOH . F 5 HOH A 74 474 215 HOH HOH . F 5 HOH A 75 475 91 HOH HOH . F 5 HOH A 76 476 199 HOH HOH . F 5 HOH A 77 477 237 HOH HOH . F 5 HOH A 78 478 22 HOH HOH . F 5 HOH A 79 479 76 HOH HOH . F 5 HOH A 80 480 36 HOH HOH . F 5 HOH A 81 481 219 HOH HOH . F 5 HOH A 82 482 82 HOH HOH . F 5 HOH A 83 483 131 HOH HOH . F 5 HOH A 84 484 96 HOH HOH . F 5 HOH A 85 485 133 HOH HOH . F 5 HOH A 86 486 33 HOH HOH . F 5 HOH A 87 487 73 HOH HOH . F 5 HOH A 88 488 40 HOH HOH . F 5 HOH A 89 489 174 HOH HOH . F 5 HOH A 90 490 152 HOH HOH . F 5 HOH A 91 491 72 HOH HOH . F 5 HOH A 92 492 77 HOH HOH . F 5 HOH A 93 493 23 HOH HOH . F 5 HOH A 94 494 61 HOH HOH . F 5 HOH A 95 495 158 HOH HOH . F 5 HOH A 96 496 2 HOH HOH . F 5 HOH A 97 497 216 HOH HOH . F 5 HOH A 98 498 231 HOH HOH . F 5 HOH A 99 499 66 HOH HOH . F 5 HOH A 100 500 87 HOH HOH . F 5 HOH A 101 501 18 HOH HOH . F 5 HOH A 102 502 122 HOH HOH . F 5 HOH A 103 503 58 HOH HOH . F 5 HOH A 104 504 191 HOH HOH . F 5 HOH A 105 505 79 HOH HOH . F 5 HOH A 106 506 104 HOH HOH . F 5 HOH A 107 507 100 HOH HOH . F 5 HOH A 108 508 120 HOH HOH . F 5 HOH A 109 509 206 HOH HOH . F 5 HOH A 110 510 12 HOH HOH . F 5 HOH A 111 511 109 HOH HOH . F 5 HOH A 112 512 129 HOH HOH . F 5 HOH A 113 513 27 HOH HOH . F 5 HOH A 114 514 121 HOH HOH . F 5 HOH A 115 515 196 HOH HOH . F 5 HOH A 116 516 221 HOH HOH . F 5 HOH A 117 517 24 HOH HOH . F 5 HOH A 118 518 69 HOH HOH . F 5 HOH A 119 519 74 HOH HOH . F 5 HOH A 120 520 127 HOH HOH . F 5 HOH A 121 521 52 HOH HOH . F 5 HOH A 122 522 177 HOH HOH . F 5 HOH A 123 523 59 HOH HOH . F 5 HOH A 124 524 35 HOH HOH . F 5 HOH A 125 525 1 HOH HOH . F 5 HOH A 126 526 205 HOH HOH . F 5 HOH A 127 527 20 HOH HOH . F 5 HOH A 128 528 26 HOH HOH . F 5 HOH A 129 529 93 HOH HOH . F 5 HOH A 130 530 60 HOH HOH . F 5 HOH A 131 531 110 HOH HOH . F 5 HOH A 132 532 163 HOH HOH . F 5 HOH A 133 533 71 HOH HOH . F 5 HOH A 134 534 111 HOH HOH . F 5 HOH A 135 535 67 HOH HOH . F 5 HOH A 136 536 31 HOH HOH . F 5 HOH A 137 537 124 HOH HOH . F 5 HOH A 138 538 30 HOH HOH . F 5 HOH A 139 539 171 HOH HOH . F 5 HOH A 140 540 64 HOH HOH . F 5 HOH A 141 541 7 HOH HOH . F 5 HOH A 142 542 160 HOH HOH . F 5 HOH A 143 543 184 HOH HOH . F 5 HOH A 144 544 65 HOH HOH . F 5 HOH A 145 545 118 HOH HOH . F 5 HOH A 146 546 130 HOH HOH . F 5 HOH A 147 547 83 HOH HOH . F 5 HOH A 148 548 203 HOH HOH . F 5 HOH A 149 549 37 HOH HOH . F 5 HOH A 150 550 213 HOH HOH . F 5 HOH A 151 551 154 HOH HOH . F 5 HOH A 152 552 180 HOH HOH . F 5 HOH A 153 553 45 HOH HOH . F 5 HOH A 154 554 3 HOH HOH . F 5 HOH A 155 555 165 HOH HOH . F 5 HOH A 156 556 94 HOH HOH . F 5 HOH A 157 557 6 HOH HOH . F 5 HOH A 158 558 44 HOH HOH . F 5 HOH A 159 559 15 HOH HOH . F 5 HOH A 160 560 235 HOH HOH . F 5 HOH A 161 561 217 HOH HOH . F 5 HOH A 162 562 113 HOH HOH . F 5 HOH A 163 563 166 HOH HOH . F 5 HOH A 164 564 226 HOH HOH . F 5 HOH A 165 565 170 HOH HOH . F 5 HOH A 166 566 181 HOH HOH . F 5 HOH A 167 567 114 HOH HOH . F 5 HOH A 168 568 173 HOH HOH . F 5 HOH A 169 569 153 HOH HOH . F 5 HOH A 170 570 149 HOH HOH . F 5 HOH A 171 571 172 HOH HOH . F 5 HOH A 172 572 138 HOH HOH . F 5 HOH A 173 573 208 HOH HOH . F 5 HOH A 174 574 197 HOH HOH . F 5 HOH A 175 575 224 HOH HOH . F 5 HOH A 176 576 105 HOH HOH . F 5 HOH A 177 577 207 HOH HOH . F 5 HOH A 178 578 179 HOH HOH . F 5 HOH A 179 579 54 HOH HOH . F 5 HOH A 180 580 159 HOH HOH . F 5 HOH A 181 581 137 HOH HOH . F 5 HOH A 182 582 200 HOH HOH . F 5 HOH A 183 583 229 HOH HOH . F 5 HOH A 184 584 50 HOH HOH . F 5 HOH A 185 585 126 HOH HOH . F 5 HOH A 186 586 233 HOH HOH . F 5 HOH A 187 587 116 HOH HOH . F 5 HOH A 188 588 198 HOH HOH . F 5 HOH A 189 589 144 HOH HOH . F 5 HOH A 190 590 51 HOH HOH . F 5 HOH A 191 591 140 HOH HOH . F 5 HOH A 192 592 19 HOH HOH . F 5 HOH A 193 593 192 HOH HOH . F 5 HOH A 194 594 218 HOH HOH . F 5 HOH A 195 595 107 HOH HOH . F 5 HOH A 196 596 141 HOH HOH . F 5 HOH A 197 597 47 HOH HOH . F 5 HOH A 198 598 139 HOH HOH . F 5 HOH A 199 599 162 HOH HOH . F 5 HOH A 200 600 57 HOH HOH . F 5 HOH A 201 601 182 HOH HOH . F 5 HOH A 202 602 189 HOH HOH . F 5 HOH A 203 603 143 HOH HOH . F 5 HOH A 204 604 201 HOH HOH . F 5 HOH A 205 605 227 HOH HOH . F 5 HOH A 206 606 220 HOH HOH . F 5 HOH A 207 607 42 HOH HOH . F 5 HOH A 208 608 176 HOH HOH . F 5 HOH A 209 609 28 HOH HOH . F 5 HOH A 210 610 48 HOH HOH . F 5 HOH A 211 611 156 HOH HOH . F 5 HOH A 212 612 148 HOH HOH . F 5 HOH A 213 613 135 HOH HOH . F 5 HOH A 214 614 125 HOH HOH . F 5 HOH A 215 615 236 HOH HOH . F 5 HOH A 216 616 90 HOH HOH . F 5 HOH A 217 617 178 HOH HOH . F 5 HOH A 218 618 228 HOH HOH . F 5 HOH A 219 619 75 HOH HOH . F 5 HOH A 220 620 134 HOH HOH . F 5 HOH A 221 621 63 HOH HOH . F 5 HOH A 222 622 85 HOH HOH . F 5 HOH A 223 623 225 HOH HOH . F 5 HOH A 224 624 16 HOH HOH . F 5 HOH A 225 625 43 HOH HOH . F 5 HOH A 226 626 157 HOH HOH . F 5 HOH A 227 627 193 HOH HOH . F 5 HOH A 228 628 175 HOH HOH . F 5 HOH A 229 629 222 HOH HOH . F 5 HOH A 230 630 136 HOH HOH . F 5 HOH A 231 631 183 HOH HOH . F 5 HOH A 232 632 92 HOH HOH . F 5 HOH A 233 633 112 HOH HOH . F 5 HOH A 234 634 202 HOH HOH . F 5 HOH A 235 635 46 HOH HOH . F 5 HOH A 236 636 188 HOH HOH . F 5 HOH A 237 637 212 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 C5' VPH . . . E 4 24.467 40.618 32.579 1 26.6 ? C5' VPH 304 A 1 HETATM 2 C C4' VPH . . . E 4 23.774 40.271 31.27 1 24.04 ? C4' VPH 304 A 1 HETATM 3 C C3' VPH . . . E 4 23.443 38.787 31.259 1 22.83 ? C3' VPH 304 A 1 HETATM 4 C C2' VPH . . . E 4 22.653 38.417 32.497 1 22.73 ? C2' VPH 304 A 1 HETATM 5 C C1' VPH . . . E 4 23.388 38.869 33.76 1 27.25 ? C1' VPH 304 A 1 HETATM 6 O O5' VPH . . . E 4 23.621 40.277 33.687 1 29.2 ? O5' VPH 304 A 1 HETATM 7 C C6' VPH . . . E 4 24.828 42.074 32.708 1 32.6 ? C6' VPH 304 A 1 HETATM 8 O O6' VPH . . . E 4 25.849 42.223 33.681 1 37.26 ? O6' VPH 304 A 1 HETATM 9 O O4' VPH . . . E 4 22.582 41.024 31.155 1 20.95 ? O4' VPH 304 A 1 HETATM 10 O O3' VPH . . . E 4 22.693 38.443 30.1 1 20.61 ? O3' VPH 304 A 1 HETATM 11 C C7 VPH . . . E 4 22.628 38.506 35.028 1 31.13 ? C7 VPH 304 A 1 HETATM 12 O O8 VPH . . . E 4 22.205 39.593 35.656 1 34.46 ? O8 VPH 304 A 1 HETATM 13 C C9 VPH . . . E 4 20.925 39.478 36.318 1 40.81 ? C9 VPH 304 A 1 HETATM 14 O O7 VPH . . . E 4 22.44 37.382 35.4 1 31.75 ? O7 VPH 304 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #