data_5EXO # _model_server_result.job_id 7VpcCrIjj6dSL8CtfdCejw _model_server_result.datetime_utc '2025-03-05 01:50:23' _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 5exo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 5EXO # _exptl.entry_id 5EXO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 394.373 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2-methoxy-5-oxidanyl-4-[(2-oxidanylidenechromen-3-yl)methoxy]oxan-3-yl] ethanoate' _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 5EXO _cell.length_a 36.796 _cell.length_b 58.411 _cell.length_c 63.928 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EXO _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C19 H22 O9' _chem_comp.formula_weight 394.373 _chem_comp.id 5SY _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2-methoxy-5-oxidanyl-4-[(2-oxidanylidenechromen-3-yl)methoxy]oxan-3-yl] ethanoate' _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 OB CF 5SY doub 1 n n C O1 5SY sing 2 n n O1 C1 5SY sing 3 n n CF OA 5SY sing 4 n n CF CB 5SY sing 5 n n OA CE 5SY sing 6 n n O2 CAC 5SY sing 7 n n O2 C2 5SY sing 8 n n CAM CAC 5SY sing 9 n n CA CB 5SY sing 10 n n CA O3 5SY sing 11 n n CB CC 5SY doub 12 n n CE CJ 5SY doub 13 n y CE CD 5SY sing 14 n y CJ CI 5SY sing 15 n y CAC OAC 5SY doub 16 n n C3 O3 5SY sing 17 n n C3 C2 5SY sing 18 n n C3 C4 5SY sing 19 n n CC CD 5SY sing 20 n n C1 C2 5SY sing 21 n n C1 O5 5SY sing 22 n n CD CG 5SY doub 23 n y CI CH 5SY doub 24 n y C5 C4 5SY sing 25 n n C5 O5 5SY sing 26 n n C5 C6 5SY sing 27 n n C4 O4 5SY sing 28 n n CG CH 5SY sing 29 n y O6 C6 5SY sing 30 n n C4 H1 5SY sing 31 n n C5 H2 5SY sing 32 n n C6 H3 5SY sing 33 n n C6 H4 5SY sing 34 n n O6 H5 5SY sing 35 n n O4 H6 5SY sing 36 n n C3 H7 5SY sing 37 n n C2 H8 5SY sing 38 n n C1 H9 5SY sing 39 n n C H10 5SY sing 40 n n C H11 5SY sing 41 n n C H12 5SY sing 42 n n CAM H13 5SY sing 43 n n CAM H14 5SY sing 44 n n CAM H15 5SY sing 45 n n CA H16 5SY sing 46 n n CA H17 5SY sing 47 n n CC H18 5SY sing 48 n n CG H19 5SY sing 49 n n CH H20 5SY sing 50 n n CI H21 5SY sing 51 n n CJ H22 5SY sing 52 n n # _atom_sites.entry_id 5EXO _atom_sites.fract_transf_matrix[1][1] 0.027177 _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] 0.01712 _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] 0.015643 _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 3 5SY A 1 302 1 5SY LIG . D 4 HOH A 1 401 149 HOH HOH . D 4 HOH A 2 402 84 HOH HOH . D 4 HOH A 3 403 129 HOH HOH . D 4 HOH A 4 404 113 HOH HOH . D 4 HOH A 5 405 156 HOH HOH . D 4 HOH A 6 406 134 HOH HOH . D 4 HOH A 7 407 107 HOH HOH . D 4 HOH A 8 408 24 HOH HOH . D 4 HOH A 9 409 52 HOH HOH . D 4 HOH A 10 410 82 HOH HOH . D 4 HOH A 11 411 126 HOH HOH . D 4 HOH A 12 412 21 HOH HOH . D 4 HOH A 13 413 41 HOH HOH . D 4 HOH A 14 414 71 HOH HOH . D 4 HOH A 15 415 56 HOH HOH . D 4 HOH A 16 416 48 HOH HOH . D 4 HOH A 17 417 23 HOH HOH . D 4 HOH A 18 418 6 HOH HOH . D 4 HOH A 19 419 178 HOH HOH . D 4 HOH A 20 420 16 HOH HOH . D 4 HOH A 21 421 117 HOH HOH . D 4 HOH A 22 422 88 HOH HOH . D 4 HOH A 23 423 135 HOH HOH . D 4 HOH A 24 424 39 HOH HOH . D 4 HOH A 25 425 55 HOH HOH . D 4 HOH A 26 426 103 HOH HOH . D 4 HOH A 27 427 29 HOH HOH . D 4 HOH A 28 428 175 HOH HOH . D 4 HOH A 29 429 168 HOH HOH . D 4 HOH A 30 430 50 HOH HOH . D 4 HOH A 31 431 139 HOH HOH . D 4 HOH A 32 432 28 HOH HOH . D 4 HOH A 33 433 125 HOH HOH . D 4 HOH A 34 434 9 HOH HOH . D 4 HOH A 35 435 97 HOH HOH . D 4 HOH A 36 436 155 HOH HOH . D 4 HOH A 37 437 22 HOH HOH . D 4 HOH A 38 438 67 HOH HOH . D 4 HOH A 39 439 8 HOH HOH . D 4 HOH A 40 440 109 HOH HOH . D 4 HOH A 41 441 154 HOH HOH . D 4 HOH A 42 442 30 HOH HOH . D 4 HOH A 43 443 106 HOH HOH . D 4 HOH A 44 444 15 HOH HOH . D 4 HOH A 45 445 95 HOH HOH . D 4 HOH A 46 446 58 HOH HOH . D 4 HOH A 47 447 3 HOH HOH . D 4 HOH A 48 448 2 HOH HOH . D 4 HOH A 49 449 171 HOH HOH . D 4 HOH A 50 450 5 HOH HOH . D 4 HOH A 51 451 36 HOH HOH . D 4 HOH A 52 452 19 HOH HOH . D 4 HOH A 53 453 102 HOH HOH . D 4 HOH A 54 454 62 HOH HOH . D 4 HOH A 55 455 147 HOH HOH . D 4 HOH A 56 456 66 HOH HOH . D 4 HOH A 57 457 64 HOH HOH . D 4 HOH A 58 458 165 HOH HOH . D 4 HOH A 59 459 10 HOH HOH . D 4 HOH A 60 460 110 HOH HOH . D 4 HOH A 61 461 49 HOH HOH . D 4 HOH A 62 462 166 HOH HOH . D 4 HOH A 63 463 152 HOH HOH . D 4 HOH A 64 464 144 HOH HOH . D 4 HOH A 65 465 43 HOH HOH . D 4 HOH A 66 466 14 HOH HOH . D 4 HOH A 67 467 78 HOH HOH . D 4 HOH A 68 468 1 HOH HOH . D 4 HOH A 69 469 13 HOH HOH . D 4 HOH A 70 470 94 HOH HOH . D 4 HOH A 71 471 146 HOH HOH . D 4 HOH A 72 472 77 HOH HOH . D 4 HOH A 73 473 47 HOH HOH . D 4 HOH A 74 474 164 HOH HOH . D 4 HOH A 75 475 17 HOH HOH . D 4 HOH A 76 476 27 HOH HOH . D 4 HOH A 77 477 73 HOH HOH . D 4 HOH A 78 478 101 HOH HOH . D 4 HOH A 79 479 124 HOH HOH . D 4 HOH A 80 480 133 HOH HOH . D 4 HOH A 81 481 7 HOH HOH . D 4 HOH A 82 482 25 HOH HOH . D 4 HOH A 83 483 18 HOH HOH . D 4 HOH A 84 484 11 HOH HOH . D 4 HOH A 85 485 115 HOH HOH . D 4 HOH A 86 486 138 HOH HOH . D 4 HOH A 87 487 42 HOH HOH . D 4 HOH A 88 488 145 HOH HOH . D 4 HOH A 89 489 69 HOH HOH . D 4 HOH A 90 490 60 HOH HOH . D 4 HOH A 91 491 33 HOH HOH . D 4 HOH A 92 492 63 HOH HOH . D 4 HOH A 93 493 79 HOH HOH . D 4 HOH A 94 494 85 HOH HOH . D 4 HOH A 95 495 86 HOH HOH . D 4 HOH A 96 496 68 HOH HOH . D 4 HOH A 97 497 45 HOH HOH . D 4 HOH A 98 498 75 HOH HOH . D 4 HOH A 99 499 54 HOH HOH . D 4 HOH A 100 500 104 HOH HOH . D 4 HOH A 101 501 72 HOH HOH . D 4 HOH A 102 502 70 HOH HOH . D 4 HOH A 103 503 105 HOH HOH . D 4 HOH A 104 504 74 HOH HOH . D 4 HOH A 105 505 170 HOH HOH . D 4 HOH A 106 506 34 HOH HOH . D 4 HOH A 107 507 20 HOH HOH . D 4 HOH A 108 508 65 HOH HOH . D 4 HOH A 109 509 173 HOH HOH . D 4 HOH A 110 510 35 HOH HOH . D 4 HOH A 111 511 96 HOH HOH . D 4 HOH A 112 512 12 HOH HOH . D 4 HOH A 113 513 37 HOH HOH . D 4 HOH A 114 514 93 HOH HOH . D 4 HOH A 115 515 87 HOH HOH . D 4 HOH A 116 516 51 HOH HOH . D 4 HOH A 117 517 26 HOH HOH . D 4 HOH A 118 518 31 HOH HOH . D 4 HOH A 119 519 38 HOH HOH . D 4 HOH A 120 520 46 HOH HOH . D 4 HOH A 121 521 32 HOH HOH . D 4 HOH A 122 522 90 HOH HOH . D 4 HOH A 123 523 160 HOH HOH . D 4 HOH A 124 524 120 HOH HOH . D 4 HOH A 125 525 172 HOH HOH . D 4 HOH A 126 526 4 HOH HOH . D 4 HOH A 127 527 57 HOH HOH . D 4 HOH A 128 528 98 HOH HOH . D 4 HOH A 129 529 174 HOH HOH . D 4 HOH A 130 530 61 HOH HOH . D 4 HOH A 131 531 40 HOH HOH . D 4 HOH A 132 532 132 HOH HOH . D 4 HOH A 133 533 159 HOH HOH . D 4 HOH A 134 534 114 HOH HOH . D 4 HOH A 135 535 89 HOH HOH . D 4 HOH A 136 536 148 HOH HOH . D 4 HOH A 137 537 59 HOH HOH . D 4 HOH A 138 538 44 HOH HOH . D 4 HOH A 139 539 169 HOH HOH . D 4 HOH A 140 540 150 HOH HOH . D 4 HOH A 141 541 130 HOH HOH . D 4 HOH A 142 542 131 HOH HOH . D 4 HOH A 143 543 128 HOH HOH . D 4 HOH A 144 544 91 HOH HOH . D 4 HOH A 145 545 92 HOH HOH . D 4 HOH A 146 546 99 HOH HOH . D 4 HOH A 147 547 76 HOH HOH . D 4 HOH A 148 548 167 HOH HOH . D 4 HOH A 149 549 83 HOH HOH . D 4 HOH A 150 550 80 HOH HOH . D 4 HOH A 151 551 162 HOH HOH . D 4 HOH A 152 552 127 HOH HOH . D 4 HOH A 153 553 158 HOH HOH . D 4 HOH A 154 554 151 HOH HOH . D 4 HOH A 155 555 161 HOH HOH . D 4 HOH A 156 556 177 HOH HOH . D 4 HOH A 157 557 137 HOH HOH . D 4 HOH A 158 558 118 HOH HOH . D 4 HOH A 159 559 81 HOH HOH . D 4 HOH A 160 560 157 HOH HOH . D 4 HOH A 161 561 53 HOH HOH . D 4 HOH A 162 562 163 HOH HOH . D 4 HOH A 163 563 140 HOH HOH . D 4 HOH A 164 564 176 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 C4 5SY . . . C 3 18.444 -6.845 -0.547 1 15.14 ? C4 5SY 302 A 1 HETATM 2 C C5 5SY . . . C 3 19.929 -6.617 -0.733 1 14.34 ? C5 5SY 302 A 1 HETATM 3 C C6 5SY . . . C 3 20.428 -5.496 0.175 1 14.26 ? C6 5SY 302 A 1 HETATM 4 O O6 5SY . . . C 3 21.818 -5.29 -0.006 1 17.13 ? O6 5SY 302 A 1 HETATM 5 O O5 5SY . . . C 3 20.687 -7.805 -0.366 1 16.07 ? O5 5SY 302 A 1 HETATM 6 O O4 5SY . . . C 3 18.116 -7.092 0.832 1 13.26 ? O4 5SY 302 A 1 HETATM 7 C C3 5SY . . . C 3 18.05 -8.04 -1.408 1 14.54 ? C3 5SY 302 A 1 HETATM 8 C C2 5SY . . . C 3 18.897 -9.228 -1.06 1 17.66 ? C2 5SY 302 A 1 HETATM 9 C C1 5SY . . . C 3 20.368 -8.957 -1.133 1 18.46 ? C1 5SY 302 A 1 HETATM 10 O O1 5SY . . . C 3 20.677 -8.635 -2.506 1 24.3 ? O1 5SY 302 A 1 HETATM 11 C C 5SY . . . C 3 22.012 -8.157 -2.673 1 25.36 ? C 5SY 302 A 1 HETATM 12 O O2 5SY . . . C 3 18.547 -10.272 -2.027 1 24.94 ? O2 5SY 302 A 1 HETATM 13 C CAC 5SY . . . C 3 18.07 -11.518 -1.451 1 32.58 ? CAC 5SY 302 A 1 HETATM 14 O OAC 5SY . . . C 3 17.323 -11.519 -0.202 1 41.37 ? OAC 5SY 302 A 1 HETATM 15 C CAM 5SY . . . C 3 18.211 -12.827 -1.948 1 36.76 ? CAM 5SY 302 A 1 HETATM 16 O O3 5SY . . . C 3 16.725 -8.426 -1.143 1 18.87 ? O3 5SY 302 A 1 HETATM 17 C CA 5SY . . . C 3 15.757 -7.777 -1.918 1 25.96 ? CA 5SY 302 A 1 HETATM 18 C CB 5SY . . . C 3 14.452 -8.54 -1.824 1 28.74 ? CB 5SY 302 A 1 HETATM 19 C CC 5SY . . . C 3 14.305 -9.704 -1.161 1 30.43 ? CC 5SY 302 A 1 HETATM 20 C CD 5SY . . . C 3 13.015 -10.357 -1.12 1 31.28 ? CD 5SY 302 A 1 HETATM 21 C CG 5SY . . . C 3 12.853 -11.557 -0.432 1 34.45 ? CG 5SY 302 A 1 HETATM 22 C CH 5SY . . . C 3 11.598 -12.185 -0.4 1 34.81 ? CH 5SY 302 A 1 HETATM 23 C CI 5SY . . . C 3 10.509 -11.593 -1.058 1 36.63 ? CI 5SY 302 A 1 HETATM 24 C CJ 5SY . . . C 3 10.673 -10.376 -1.752 1 37.03 ? CJ 5SY 302 A 1 HETATM 25 C CE 5SY . . . C 3 11.938 -9.764 -1.776 1 34.16 ? CE 5SY 302 A 1 HETATM 26 O OA 5SY . . . C 3 12.124 -8.566 -2.448 1 35.69 ? OA 5SY 302 A 1 HETATM 27 C CF 5SY . . . C 3 13.345 -7.95 -2.488 1 33.55 ? CF 5SY 302 A 1 HETATM 28 O OB 5SY . . . C 3 13.566 -6.827 -3.111 1 36.13 ? OB 5SY 302 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #