data_5YIF
#
_model_server_result.job_id            jb5UzRg1f6BtPoReYFOEaQ 
_model_server_result.datetime_utc      '2025-06-17 01:49:52' 
_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          5yif 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":501}' 
#
_entry.id    5YIF 
#
_exptl.entry_id    5YIF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              250.203 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R,4aR,6R,7R,8R,8aR)-2-methyl-6,7,8-tris(oxidanyl)-4,4a,6,7,8,8a-hexahydropyrano[3,2-d][1,3]dioxine-2-carboxylic acid' 
_entity.pdbx_number_of_molecules    2 
_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         120 
_cell.entry_id            5YIF 
_cell.length_a            114.78 
_cell.length_b            114.78 
_cell.length_c            150.434 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YIF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 2 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C9 H14 O8' 
_chem_comp.formula_weight    250.203 
_chem_comp.id                8VR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2R,4aR,6R,7R,8R,8aR)-2-methyl-6,7,8-tris(oxidanyl)-4,4a,6,7,8,8a-hexahydropyrano[3,2-d][1,3]dioxine-2-carboxylic acid' 
_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 8VR sing 1 n n 
C3 C4 8VR sing 2 n n 
C3 C2 8VR sing 3 n n 
O8B C8 8VR doub 4 n n 
O4 C4 8VR sing 5 n n 
O4 C7 8VR sing 6 n n 
O2 C2 8VR sing 7 n n 
C4 C5 8VR sing 8 n n 
C2 C1 8VR sing 9 n n 
C8 C7 8VR sing 10 n n 
C8 O8A 8VR sing 11 n n 
C9 C7 8VR sing 12 n n 
C7 O6 8VR sing 13 n n 
C5 O5 8VR sing 14 n n 
C5 C6 8VR sing 15 n n 
C1 O5 8VR sing 16 n n 
C1 O1 8VR sing 17 n n 
O6 C6 8VR sing 18 n n 
C1 H1 8VR sing 19 n n 
C2 H2 8VR sing 20 n n 
C3 H3 8VR sing 21 n n 
C4 H4 8VR sing 22 n n 
C5 H5 8VR sing 23 n n 
C6 H6 8VR sing 24 n n 
C6 H7 8VR sing 25 n n 
C9 H8 8VR sing 26 n n 
C9 H9 8VR sing 27 n n 
C9 H10 8VR sing 28 n n 
O1 H11 8VR sing 29 n n 
O2 H12 8VR sing 30 n n 
O3 H13 8VR sing 31 n n 
O8A H14 8VR sing 32 n n 
#
_atom_sites.entry_id                     5YIF 
_atom_sites.fract_transf_matrix[1][1]    0.008712 
_atom_sites.fract_transf_matrix[1][2]    0.00503 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01006 
_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]    0.006647 
_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
C 2 8VR A 1 501 1 8VR PVG . 
D 2 8VR B 1 501 2 8VR PVG . 
E 3 HOH A 1 601 108 HOH HOH . 
E 3 HOH A 2 602 23 HOH HOH . 
E 3 HOH A 3 603 68 HOH HOH . 
E 3 HOH A 4 604 167 HOH HOH . 
E 3 HOH A 5 605 112 HOH HOH . 
E 3 HOH A 6 606 111 HOH HOH . 
E 3 HOH A 7 607 165 HOH HOH . 
E 3 HOH A 8 608 98 HOH HOH . 
E 3 HOH A 9 609 116 HOH HOH . 
E 3 HOH A 10 610 164 HOH HOH . 
E 3 HOH A 11 611 159 HOH HOH . 
E 3 HOH A 12 612 15 HOH HOH . 
E 3 HOH A 13 613 140 HOH HOH . 
E 3 HOH A 14 614 119 HOH HOH . 
E 3 HOH A 15 615 101 HOH HOH . 
E 3 HOH A 16 616 34 HOH HOH . 
E 3 HOH A 17 617 80 HOH HOH . 
E 3 HOH A 18 618 131 HOH HOH . 
E 3 HOH A 19 619 148 HOH HOH . 
E 3 HOH A 20 620 90 HOH HOH . 
E 3 HOH A 21 621 78 HOH HOH . 
E 3 HOH A 22 622 60 HOH HOH . 
E 3 HOH A 23 623 125 HOH HOH . 
E 3 HOH A 24 624 58 HOH HOH . 
E 3 HOH A 25 625 13 HOH HOH . 
E 3 HOH A 26 626 86 HOH HOH . 
E 3 HOH A 27 627 39 HOH HOH . 
E 3 HOH A 28 628 156 HOH HOH . 
E 3 HOH A 29 629 139 HOH HOH . 
E 3 HOH A 30 630 88 HOH HOH . 
E 3 HOH A 31 631 73 HOH HOH . 
E 3 HOH A 32 632 1 HOH HOH . 
E 3 HOH A 33 633 129 HOH HOH . 
E 3 HOH A 34 634 5 HOH HOH . 
E 3 HOH A 35 635 30 HOH HOH . 
E 3 HOH A 36 636 6 HOH HOH . 
E 3 HOH A 37 637 11 HOH HOH . 
E 3 HOH A 38 638 144 HOH HOH . 
E 3 HOH A 39 639 32 HOH HOH . 
E 3 HOH A 40 640 145 HOH HOH . 
E 3 HOH A 41 641 19 HOH HOH . 
E 3 HOH A 42 642 14 HOH HOH . 
E 3 HOH A 43 643 75 HOH HOH . 
E 3 HOH A 44 644 146 HOH HOH . 
E 3 HOH A 45 645 48 HOH HOH . 
E 3 HOH A 46 646 113 HOH HOH . 
E 3 HOH A 47 647 43 HOH HOH . 
E 3 HOH A 48 648 40 HOH HOH . 
E 3 HOH A 49 649 24 HOH HOH . 
E 3 HOH A 50 650 21 HOH HOH . 
E 3 HOH A 51 651 84 HOH HOH . 
E 3 HOH A 52 652 47 HOH HOH . 
E 3 HOH A 53 653 135 HOH HOH . 
E 3 HOH A 54 654 128 HOH HOH . 
E 3 HOH A 55 655 3 HOH HOH . 
E 3 HOH A 56 656 55 HOH HOH . 
E 3 HOH A 57 657 35 HOH HOH . 
E 3 HOH A 58 658 45 HOH HOH . 
E 3 HOH A 59 659 134 HOH HOH . 
E 3 HOH A 60 660 38 HOH HOH . 
E 3 HOH A 61 661 163 HOH HOH . 
E 3 HOH A 62 662 142 HOH HOH . 
E 3 HOH A 63 663 28 HOH HOH . 
E 3 HOH A 64 664 160 HOH HOH . 
E 3 HOH A 65 665 77 HOH HOH . 
E 3 HOH A 66 666 49 HOH HOH . 
E 3 HOH A 67 667 81 HOH HOH . 
E 3 HOH A 68 668 51 HOH HOH . 
E 3 HOH A 69 669 29 HOH HOH . 
E 3 HOH A 70 670 76 HOH HOH . 
E 3 HOH A 71 671 71 HOH HOH . 
E 3 HOH A 72 672 141 HOH HOH . 
E 3 HOH A 73 673 37 HOH HOH . 
E 3 HOH A 74 674 83 HOH HOH . 
E 3 HOH A 75 675 153 HOH HOH . 
E 3 HOH A 76 676 133 HOH HOH . 
E 3 HOH A 77 677 67 HOH HOH . 
E 3 HOH A 78 678 99 HOH HOH . 
E 3 HOH A 79 679 93 HOH HOH . 
E 3 HOH A 80 680 53 HOH HOH . 
F 3 HOH B 1 601 107 HOH HOH . 
F 3 HOH B 2 602 117 HOH HOH . 
F 3 HOH B 3 603 124 HOH HOH . 
F 3 HOH B 4 604 4 HOH HOH . 
F 3 HOH B 5 605 85 HOH HOH . 
F 3 HOH B 6 606 9 HOH HOH . 
F 3 HOH B 7 607 97 HOH HOH . 
F 3 HOH B 8 608 152 HOH HOH . 
F 3 HOH B 9 609 110 HOH HOH . 
F 3 HOH B 10 610 155 HOH HOH . 
F 3 HOH B 11 611 132 HOH HOH . 
F 3 HOH B 12 612 109 HOH HOH . 
F 3 HOH B 13 613 147 HOH HOH . 
F 3 HOH B 14 614 8 HOH HOH . 
F 3 HOH B 15 615 64 HOH HOH . 
F 3 HOH B 16 616 26 HOH HOH . 
F 3 HOH B 17 617 33 HOH HOH . 
F 3 HOH B 18 618 2 HOH HOH . 
F 3 HOH B 19 619 69 HOH HOH . 
F 3 HOH B 20 620 17 HOH HOH . 
F 3 HOH B 21 621 74 HOH HOH . 
F 3 HOH B 22 622 89 HOH HOH . 
F 3 HOH B 23 623 87 HOH HOH . 
F 3 HOH B 24 624 118 HOH HOH . 
F 3 HOH B 25 625 79 HOH HOH . 
F 3 HOH B 26 626 161 HOH HOH . 
F 3 HOH B 27 627 65 HOH HOH . 
F 3 HOH B 28 628 46 HOH HOH . 
F 3 HOH B 29 629 120 HOH HOH . 
F 3 HOH B 30 630 136 HOH HOH . 
F 3 HOH B 31 631 92 HOH HOH . 
F 3 HOH B 32 632 10 HOH HOH . 
F 3 HOH B 33 633 12 HOH HOH . 
F 3 HOH B 34 634 52 HOH HOH . 
F 3 HOH B 35 635 50 HOH HOH . 
F 3 HOH B 36 636 20 HOH HOH . 
F 3 HOH B 37 637 137 HOH HOH . 
F 3 HOH B 38 638 166 HOH HOH . 
F 3 HOH B 39 639 162 HOH HOH . 
F 3 HOH B 40 640 44 HOH HOH . 
F 3 HOH B 41 641 91 HOH HOH . 
F 3 HOH B 42 642 36 HOH HOH . 
F 3 HOH B 43 643 102 HOH HOH . 
F 3 HOH B 44 644 149 HOH HOH . 
F 3 HOH B 45 645 114 HOH HOH . 
F 3 HOH B 46 646 16 HOH HOH . 
F 3 HOH B 47 647 41 HOH HOH . 
F 3 HOH B 48 648 18 HOH HOH . 
F 3 HOH B 49 649 54 HOH HOH . 
F 3 HOH B 50 650 123 HOH HOH . 
F 3 HOH B 51 651 31 HOH HOH . 
F 3 HOH B 52 652 150 HOH HOH . 
F 3 HOH B 53 653 143 HOH HOH . 
F 3 HOH B 54 654 95 HOH HOH . 
F 3 HOH B 55 655 82 HOH HOH . 
F 3 HOH B 56 656 42 HOH HOH . 
F 3 HOH B 57 657 130 HOH HOH . 
F 3 HOH B 58 658 121 HOH HOH . 
F 3 HOH B 59 659 70 HOH HOH . 
F 3 HOH B 60 660 56 HOH HOH . 
F 3 HOH B 61 661 57 HOH HOH . 
F 3 HOH B 62 662 96 HOH HOH . 
F 3 HOH B 63 663 127 HOH HOH . 
F 3 HOH B 64 664 151 HOH HOH . 
F 3 HOH B 65 665 138 HOH HOH . 
F 3 HOH B 66 666 122 HOH HOH . 
F 3 HOH B 67 667 63 HOH HOH . 
F 3 HOH B 68 668 100 HOH HOH . 
F 3 HOH B 69 669 157 HOH HOH . 
F 3 HOH B 70 670 72 HOH HOH . 
F 3 HOH B 71 671 62 HOH HOH . 
F 3 HOH B 72 672 22 HOH HOH . 
F 3 HOH B 73 673 25 HOH HOH . 
F 3 HOH B 74 674 27 HOH HOH . 
F 3 HOH B 75 675 61 HOH HOH . 
F 3 HOH B 76 676 104 HOH HOH . 
F 3 HOH B 77 677 7 HOH HOH . 
F 3 HOH B 78 678 115 HOH HOH . 
F 3 HOH B 79 679 94 HOH HOH . 
F 3 HOH B 80 680 103 HOH HOH . 
F 3 HOH B 81 681 126 HOH HOH . 
F 3 HOH B 82 682 154 HOH HOH . 
F 3 HOH B 83 683 158 HOH HOH . 
F 3 HOH B 84 684 106 HOH HOH . 
F 3 HOH B 85 685 105 HOH HOH . 
F 3 HOH B 86 686 59 HOH HOH . 
F 3 HOH B 87 687 66 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 C1 8VR . . . C 2 4.525 -38.762 -4.396 1 34.44 ? C1 8VR 501 A 1 
HETATM 2 C C2 8VR . . . C 2 4.822 -38.496 -5.791 1 34.77 ? C2 8VR 501 A 1 
HETATM 3 C C3 8VR . . . C 2 4.28 -39.636 -6.633 1 37.86 ? C3 8VR 501 A 1 
HETATM 4 C C4 8VR . . . C 2 4.457 -41.042 -5.965 1 38.08 ? C4 8VR 501 A 1 
HETATM 5 C C5 8VR . . . C 2 4.419 -40.824 -4.473 1 35.67 ? C5 8VR 501 A 1 
HETATM 6 C C6 8VR . . . C 2 4.763 -42.045 -3.77 1 37.64 ? C6 8VR 501 A 1 
HETATM 7 C C7 8VR . . . C 2 6.495 -42.402 -5.198 1 43.38 ? C7 8VR 501 A 1 
HETATM 8 C C8 8VR . . . C 2 7.002 -43.79 -5.438 1 32.18 ? C8 8VR 501 A 1 
HETATM 9 C C9 8VR . . . C 2 7.731 -41.492 -5.203 1 48.2 ? C9 8VR 501 A 1 
HETATM 10 O O1 8VR . . . C 2 5.098 -37.901 -3.555 1 34.86 ? O1 8VR 501 A 1 
HETATM 11 O O2 8VR . . . C 2 4.12 -37.409 -6.115 1 30.78 ? O2 8VR 501 A 1 
HETATM 12 O O3 8VR . . . C 2 4.785 -39.541 -7.875 1 40.16 ? O3 8VR 501 A 1 
HETATM 13 O O4 8VR . . . C 2 5.552 -41.894 -6.328 1 41.58 ? O4 8VR 501 A 1 
HETATM 14 O O5 8VR . . . C 2 5.227 -39.791 -4.075 1 34.14 ? O5 8VR 501 A 1 
HETATM 15 O O6 8VR . . . C 2 6.037 -42.341 -3.907 1 36.13 ? O6 8VR 501 A 1 
HETATM 16 O O8A 8VR . . . C 2 7.555 -44.405 -4.601 1 27.97 ? O8A 8VR 501 A 1 
HETATM 17 O O8B 8VR . . . C 2 6.962 -44.184 -6.541 1 43.01 ? O8B 8VR 501 A 1 
#
_model_server_stats.io_time_ms              65 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           17 
#