data_8K08
#
_model_server_result.job_id            F3DWfoTCNZ2qBLXYkevIPQ 
_model_server_result.datetime_utc      '2025-07-05 04:01:10' 
_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          8k08 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    8K08 
#
_exptl.entry_id    8K08 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              622.873 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'Ginsenoside Rh2' 
_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         90 
_cell.entry_id            8K08 
_cell.length_a            70.349 
_cell.length_b            90.203 
_cell.length_c            155.873 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8K08 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 1 1 
B,D 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           'C36 H62 O8' 
_chem_comp.formula_weight    622.873 
_chem_comp.id                8YG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'Ginsenoside Rh2' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     (2R,3S,4S,5R,6R)-2-(hydroxymethyl)-6-[[(3S,5R,8R,9R,10R,12R,13R,14R,17S)-4,4,8,10,14-pentamethyl-17-[(2S)-6-methyl-2-oxidanyl-hept-5-en-2-yl]-12-oxidanyl-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-yl]oxy]oxane-3,4,5-triol 
#
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
C43 C41 8YG sing 1 n n 
C44 C41 8YG sing 2 n n 
C41 C37 8YG doub 3 n n 
C37 C34 8YG sing 4 n n 
C34 C32 8YG sing 5 n n 
O03 C29 8YG sing 6 n n 
O01 C18 8YG sing 7 n n 
C32 C29 8YG sing 8 n n 
C29 C33 8YG sing 9 n n 
C29 C17 8YG sing 10 n n 
C18 C16 8YG sing 11 n n 
C18 C13 8YG sing 12 n n 
C16 C11 8YG sing 13 n n 
C17 C13 8YG sing 14 n n 
C17 C22 8YG sing 15 n n 
C13 C10 8YG sing 16 n n 
O06 C38 8YG sing 17 n n 
C23 C28 8YG sing 18 n n 
C23 C12 8YG sing 19 n n 
C11 C12 8YG sing 20 n n 
C11 C09 8YG sing 21 n n 
C22 C19 8YG sing 22 n n 
C28 C27 8YG sing 23 n n 
C26 C12 8YG sing 24 n n 
C10 C25 8YG sing 25 n n 
C10 C09 8YG sing 26 n n 
C10 C19 8YG sing 27 n n 
C12 C14 8YG sing 28 n n 
C24 C09 8YG sing 29 n n 
O07 C40 8YG sing 30 n n 
C38 C40 8YG sing 31 n n 
C38 C36 8YG sing 32 n n 
C40 C39 8YG sing 33 n n 
C09 C15 8YG sing 34 n n 
C36 O05 8YG sing 35 n n 
C36 C35 8YG sing 36 n n 
C27 O02 8YG sing 37 n n 
C27 C21 8YG sing 38 n n 
O08 C42 8YG sing 39 n n 
C14 C21 8YG sing 40 n n 
C14 C20 8YG sing 41 n n 
C42 C39 8YG sing 42 n n 
O02 C35 8YG sing 43 n n 
C39 O04 8YG sing 44 n n 
C35 O04 8YG sing 45 n n 
C15 C20 8YG sing 46 n n 
C21 C30 8YG sing 47 n n 
C21 C31 8YG sing 48 n n 
C13 H1 8YG sing 49 n n 
C15 H2 8YG sing 50 n n 
C15 H3 8YG sing 51 n n 
C17 H4 8YG sing 52 n n 
C20 H5 8YG sing 53 n n 
C20 H6 8YG sing 54 n n 
C22 H7 8YG sing 55 n n 
C22 H8 8YG sing 56 n n 
C24 H9 8YG sing 57 n n 
C24 H10 8YG sing 58 n n 
C24 H11 8YG sing 59 n n 
C26 H12 8YG sing 60 n n 
C26 H13 8YG sing 61 n n 
C26 H14 8YG sing 62 n n 
C28 H15 8YG sing 63 n n 
C28 H16 8YG sing 64 n n 
C11 H17 8YG sing 65 n n 
C14 H18 8YG sing 66 n n 
C16 H19 8YG sing 67 n n 
C16 H20 8YG sing 68 n n 
C18 H21 8YG sing 69 n n 
C19 H22 8YG sing 70 n n 
C19 H23 8YG sing 71 n n 
C23 H24 8YG sing 72 n n 
C23 H25 8YG sing 73 n n 
C25 H26 8YG sing 74 n n 
C25 H27 8YG sing 75 n n 
C25 H28 8YG sing 76 n n 
C27 H29 8YG sing 77 n n 
C30 H30 8YG sing 78 n n 
C30 H31 8YG sing 79 n n 
C30 H32 8YG sing 80 n n 
C31 H33 8YG sing 81 n n 
C31 H34 8YG sing 82 n n 
C31 H35 8YG sing 83 n n 
C32 H36 8YG sing 84 n n 
C32 H37 8YG sing 85 n n 
C33 H38 8YG sing 86 n n 
C33 H39 8YG sing 87 n n 
C33 H40 8YG sing 88 n n 
C34 H41 8YG sing 89 n n 
C34 H42 8YG sing 90 n n 
C35 H43 8YG sing 91 n n 
C36 H44 8YG sing 92 n n 
C37 H45 8YG sing 93 n n 
C38 H46 8YG sing 94 n n 
C39 H47 8YG sing 95 n n 
C40 H48 8YG sing 96 n n 
C42 H49 8YG sing 97 n n 
C42 H50 8YG sing 98 n n 
C43 H51 8YG sing 99 n n 
C43 H52 8YG sing 100 n n 
C43 H53 8YG sing 101 n n 
C44 H54 8YG sing 102 n n 
C44 H55 8YG sing 103 n n 
C44 H56 8YG sing 104 n n 
O01 H57 8YG sing 105 n n 
O03 H58 8YG sing 106 n n 
O05 H59 8YG sing 107 n n 
O06 H60 8YG sing 108 n n 
O07 H61 8YG sing 109 n n 
O08 H62 8YG sing 110 n n 
#
_atom_sites.entry_id                     8K08 
_atom_sites.fract_transf_matrix[1][1]    0.014215 
_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]    0.011086 
_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]    0.006415 
_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 8YG A 1 501 501 8YG LIG . 
D 2 8YG B 1 501 501 8YG LIG . 
#
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 C10 8YG . . . D 2 -51.101 -7.085 -15.625 1 90.24 ? C10 8YG 501 B 1 
HETATM 2 C C13 8YG . . . D 2 -51.38 -8.631 -15.276 1 96.87 ? C13 8YG 501 B 1 
HETATM 3 C C15 8YG . . . D 2 -51.623 -4.653 -14.819 1 98.53 ? C15 8YG 501 B 1 
HETATM 4 C C17 8YG . . . D 2 -50.942 -9.423 -16.654 1 103.11 ? C17 8YG 501 B 1 
HETATM 5 C C20 8YG . . . D 2 -51.386 -3.644 -13.601 1 97.37 ? C20 8YG 501 B 1 
HETATM 6 C C21 8YG . . . D 2 -49.68 -2.988 -11.564 1 99.62 ? C21 8YG 501 B 1 
HETATM 7 C C22 8YG . . . D 2 -50.982 -8.293 -17.786 1 94.67 ? C22 8YG 501 B 1 
HETATM 8 C C24 8YG . . . D 2 -53.197 -6.542 -14.379 1 100.62 ? C24 8YG 501 B 1 
HETATM 9 C C26 8YG . . . D 2 -52.241 -5.225 -11.377 1 104.19 ? C26 8YG 501 B 1 
HETATM 10 C C28 8YG . . . D 2 -49.911 -4.766 -9.7 1 101.58 ? C28 8YG 501 B 1 
HETATM 11 C C09 8YG . . . D 2 -51.685 -6.182 -14.476 1 94.89 ? C09 8YG 501 B 1 
HETATM 12 C C11 8YG . . . D 2 -50.838 -6.564 -13.149 1 98.97 ? C11 8YG 501 B 1 
HETATM 13 C C12 8YG . . . D 2 -50.83 -5.444 -11.964 1 101.17 ? C12 8YG 501 B 1 
HETATM 14 C C14 8YG . . . D 2 -50.257 -4.125 -12.603 1 101.29 ? C14 8YG 501 B 1 
HETATM 15 C C16 8YG . . . D 2 -51.26 -8.002 -12.712 1 100.59 ? C16 8YG 501 B 1 
HETATM 16 C C18 8YG . . . D 2 -50.792 -9.03 -13.853 1 98.41 ? C18 8YG 501 B 1 
HETATM 17 C C19 8YG . . . D 2 -51.576 -7.004 -17.11 1 93.35 ? C19 8YG 501 B 1 
HETATM 18 C C23 8YG . . . D 2 -50.021 -5.898 -10.74 1 99.67 ? C23 8YG 501 B 1 
HETATM 19 C C25 8YG . . . D 2 -49.578 -6.846 -15.678 1 97.22 ? C25 8YG 501 B 1 
HETATM 20 C C27 8YG . . . D 2 -49.03 -3.59 -10.222 1 104.34 ? C27 8YG 501 B 1 
HETATM 21 C C29 8YG . . . D 2 -51.925 -10.523 -16.966 1 101.31 ? C29 8YG 501 B 1 
HETATM 22 C C30 8YG . . . D 2 -50.787 -1.973 -11.183 1 101.23 ? C30 8YG 501 B 1 
HETATM 23 C C31 8YG . . . D 2 -48.568 -2.214 -12.285 1 96.07 ? C31 8YG 501 B 1 
HETATM 24 C C32 8YG . . . D 2 -52.556 -10.377 -18.427 1 97.36 ? C32 8YG 501 B 1 
HETATM 25 C C33 8YG . . . D 2 -51.135 -11.886 -16.928 1 95.65 ? C33 8YG 501 B 1 
HETATM 26 C C34 8YG . . . D 2 -54.112 -10.562 -18.457 1 105.42 ? C34 8YG 501 B 1 
HETATM 27 C C35 8YG . . . D 2 -48.074 -3 -8.034 1 121.6 ? C35 8YG 501 B 1 
HETATM 28 C C36 8YG . . . D 2 -47.363 -1.837 -7.29 1 119.34 ? C36 8YG 501 B 1 
HETATM 29 C C37 8YG . . . D 2 -54.826 -10.996 -19.748 1 118.07 ? C37 8YG 501 B 1 
HETATM 30 C C38 8YG . . . D 2 -46.735 -2.311 -5.971 1 127.15 ? C38 8YG 501 B 1 
HETATM 31 C C39 8YG . . . D 2 -48.345 -4.288 -6.057 1 131.13 ? C39 8YG 501 B 1 
HETATM 32 C C40 8YG . . . D 2 -47.639 -3.244 -5.149 1 132.93 ? C40 8YG 501 B 1 
HETATM 33 C C41 8YG . . . D 2 -55.087 -12.23 -20.186 1 122.03 ? C41 8YG 501 B 1 
HETATM 34 C C42 8YG . . . D 2 -49.401 -5.099 -5.27 1 129.01 ? C42 8YG 501 B 1 
HETATM 35 C C43 8YG . . . D 2 -55.818 -12.566 -21.506 1 123.4 ? C43 8YG 501 B 1 
HETATM 36 C C44 8YG . . . D 2 -54.659 -13.483 -19.371 1 114.99 ? C44 8YG 501 B 1 
HETATM 37 O O01 8YG . . . D 2 -51.293 -10.312 -13.558 1 96.96 ? O01 8YG 501 B 1 
HETATM 38 O O02 8YG . . . D 2 -48.835 -2.613 -9.168 1 115.91 ? O02 8YG 501 B 1 
HETATM 39 O O03 8YG . . . D 2 -52.916 -10.464 -16.007 1 100.31 ? O03 8YG 501 B 1 
HETATM 40 O O04 8YG . . . D 2 -48.961 -3.598 -7.111 1 127.68 ? O04 8YG 501 B 1 
HETATM 41 O O05 8YG . . . D 2 -46.353 -1.317 -8.102 1 115.23 ? O05 8YG 501 B 1 
HETATM 42 O O06 8YG . . . D 2 -46.424 -1.17 -5.164 1 129.31 ? O06 8YG 501 B 1 
HETATM 43 O O07 8YG . . . D 2 -46.952 -3.871 -4.098 1 133.11 ? O07 8YG 501 B 1 
HETATM 44 O O08 8YG . . . D 2 -50.197 -4.208 -4.536 1 129.89 ? O08 8YG 501 B 1 
#
_model_server_stats.io_time_ms              76 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           227 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           44 
#