data_4ZYR
#
_model_server_result.job_id            67Mku5AoV-nTh3bRtKTsQQ 
_model_server_result.datetime_utc      '2025-01-07 02:59:25' 
_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          4zyr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    4ZYR 
#
_exptl.entry_id    4ZYR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              306.395 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            'nonyl beta-D-glucopyranoside' 
_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            4ZYR 
_cell.length_a            103.15 
_cell.length_b            121.99 
_cell.length_c            266.09 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4ZYR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 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,D 1 1 
B,E,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
? 3 D N N 
? 3 F N N 
#
_chem_comp.formula           'C15 H30 O6' 
_chem_comp.formula_weight    306.395 
_chem_comp.id                BNG 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              'nonyl beta-D-glucopyranoside' 
_chem_comp.type              d-saccharide 
_chem_comp.pdbx_synonyms     'Beta-NONYLGLUCOSIDE;nonyl beta-D-glucoside;nonyl D-glucoside;nonyl glucoside' 
#
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
C1 C2 BNG sing 107 n n 
C1 O1 BNG sing 108 n n 
C1 O5 BNG sing 109 n n 
C1 H1 BNG sing 110 n n 
C2 C3 BNG sing 111 n n 
C2 O2 BNG sing 112 n n 
C2 H2 BNG sing 113 n n 
C3 C4 BNG sing 114 n n 
C3 O3 BNG sing 115 n n 
C3 H3 BNG sing 116 n n 
C4 C5 BNG sing 117 n n 
C4 O4 BNG sing 118 n n 
C4 H4 BNG sing 119 n n 
C5 C6 BNG sing 120 n n 
C5 O5 BNG sing 121 n n 
C5 H5 BNG sing 122 n n 
C6 O6 BNG sing 123 n n 
C6 H61 BNG sing 124 n n 
C6 H62 BNG sing 125 n n 
C1' C2' BNG sing 126 n n 
C1' O1 BNG sing 127 n n 
C1' "H1'1" BNG sing 128 n n 
C1' "H1'2" BNG sing 129 n n 
C2' C3' BNG sing 130 n n 
C2' "H2'1" BNG sing 131 n n 
C2' "H2'2" BNG sing 132 n n 
C3' C4' BNG sing 133 n n 
C3' "H3'1" BNG sing 134 n n 
C3' "H3'2" BNG sing 135 n n 
C4' C5' BNG sing 136 n n 
C4' "H4'1" BNG sing 137 n n 
C4' "H4'2" BNG sing 138 n n 
C5' C6' BNG sing 139 n n 
C5' "H5'1" BNG sing 140 n n 
C5' "H5'2" BNG sing 141 n n 
C6' C7' BNG sing 142 n n 
C6' "H6'1" BNG sing 143 n n 
C6' "H6'2" BNG sing 144 n n 
C7' C8' BNG sing 145 n n 
C7' "H7'1" BNG sing 146 n n 
C7' "H7'2" BNG sing 147 n n 
C8' C9' BNG sing 148 n n 
C8' "H8'1" BNG sing 149 n n 
C8' "H8'2" BNG sing 150 n n 
C9' "H9'1" BNG sing 151 n n 
C9' "H9'2" BNG sing 152 n n 
C9' "H9'3" BNG sing 153 n n 
O2 HO2 BNG sing 154 n n 
O3 HO3 BNG sing 155 n n 
O4 HO4 BNG sing 156 n n 
O6 HO6 BNG sing 157 n n 
#
_pdbx_chem_comp_identifier.comp_id            BNG 
_pdbx_chem_comp_identifier.identifier         b-nonylglucoside 
_pdbx_chem_comp_identifier.type               'IUPAC CARBOHYDRATE SYMBOL' 
_pdbx_chem_comp_identifier.program            PDB-CARE 
_pdbx_chem_comp_identifier.program_version    1 
#
_atom_sites.entry_id                     4ZYR 
_atom_sites.fract_transf_matrix[1][1]    0.009695 
_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]    0.008197 
_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]    0.003758 
_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 9PG A 1 501 1 9PG NPG . 
D 3 BNG A 1 502 1 BNG BNG . 
E 2 9PG B 1 501 1 9PG NPG . 
F 3 BNG B 1 502 1 BNG BNG . 
#
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 BNG . . . D 3 9.478 -39.988 43.638 1 168.38 ? C1 BNG 502 A 1 
HETATM 2 C C2 BNG . . . D 3 8.219 -40.085 44.497 1 168.38 ? C2 BNG 502 A 1 
HETATM 3 C C3 BNG . . . D 3 7.313 -38.88 44.27 1 168.38 ? C3 BNG 502 A 1 
HETATM 4 C C4 BNG . . . D 3 8.081 -37.565 44.345 1 168.38 ? C4 BNG 502 A 1 
HETATM 5 C C5 BNG . . . D 3 9.378 -37.622 43.535 1 168.38 ? C5 BNG 502 A 1 
HETATM 6 C C6 BNG . . . D 3 10.234 -36.368 43.709 1 168.38 ? C6 BNG 502 A 1 
HETATM 7 C C1' BNG . . . D 3 11.423 -41.211 42.973 1 168.38 ? C1' BNG 502 A 1 
HETATM 8 C C2' BNG . . . D 3 12.195 -42.501 43.246 1 168.38 ? C2' BNG 502 A 1 
HETATM 9 C C3' BNG . . . D 3 13.389 -42.619 42.305 1 168.38 ? C3' BNG 502 A 1 
HETATM 10 C C4' BNG . . . D 3 14.285 -43.811 42.64 1 168.38 ? C4' BNG 502 A 1 
HETATM 11 C C5' BNG . . . D 3 15.56 -43.732 41.806 1 168.38 ? C5' BNG 502 A 1 
HETATM 12 C C6' BNG . . . D 3 16.404 -45 41.876 1 168.38 ? C6' BNG 502 A 1 
HETATM 13 C C7' BNG . . . D 3 17.567 -44.894 40.895 1 168.38 ? C7' BNG 502 A 1 
HETATM 14 C C8' BNG . . . D 3 18.382 -46.18 40.849 1 168.38 ? C8' BNG 502 A 1 
HETATM 15 C C9' BNG . . . D 3 19.445 -46.12 39.771 1 168.38 ? C9' BNG 502 A 1 
HETATM 16 O O1 BNG . . . D 3 10.348 -41.09 43.908 1 168.38 ? O1 BNG 502 A 1 
HETATM 17 O O2 BNG . . . D 3 7.492 -41.279 44.179 1 168.38 ? O2 BNG 502 A 1 
HETATM 18 O O3 BNG . . . D 3 6.286 -38.876 45.267 1 168.38 ? O3 BNG 502 A 1 
HETATM 19 O O4 BNG . . . D 3 7.22 -36.524 43.863 1 168.38 ? O4 BNG 502 A 1 
HETATM 20 O O5 BNG . . . D 3 10.142 -38.76 43.939 1 168.38 ? O5 BNG 502 A 1 
HETATM 21 O O6 BNG . . . D 3 11.535 -36.6 43.156 1 168.38 ? O6 BNG 502 A 1 
HETATM 22 H H1 BNG . . . D 3 9.182 -39.999 42.579 1 16.07 ? H1 BNG 502 A 1 
HETATM 23 H H2 BNG . . . D 3 8.518 -40.103 45.555 1 16.07 ? H2 BNG 502 A 1 
HETATM 24 H H3 BNG . . . D 3 6.86 -38.965 43.272 1 16.07 ? H3 BNG 502 A 1 
HETATM 25 H H4 BNG . . . D 3 8.336 -37.372 45.397 1 16.07 ? H4 BNG 502 A 1 
HETATM 26 H H5 BNG . . . D 3 9.117 -37.716 42.472 1 16.07 ? H5 BNG 502 A 1 
HETATM 27 H H61 BNG . . . D 3 10.321 -36.125 44.77 1 16.07 ? H61 BNG 502 A 1 
HETATM 28 H H62 BNG . . . D 3 9.761 -35.524 43.202 1 16.07 ? H62 BNG 502 A 1 
HETATM 29 H "H1'1" BNG . . . D 3 12.093 -40.353 43.068 1 16.07 ? "H1'1" BNG 502 A 1 
HETATM 30 H "H1'2" BNG . . . D 3 11.028 -41.225 41.956 1 16.07 ? "H1'2" BNG 502 A 1 
HETATM 31 H "H2'1" BNG . . . D 3 11.533 -43.358 43.107 1 16.07 ? "H2'1" BNG 502 A 1 
HETATM 32 H "H2'2" BNG . . . D 3 12.543 -42.507 44.281 1 16.07 ? "H2'2" BNG 502 A 1 
HETATM 33 H "H3'1" BNG . . . D 3 13.979 -41.702 42.358 1 16.07 ? "H3'1" BNG 502 A 1 
HETATM 34 H "H3'2" BNG . . . D 3 13.028 -42.72 41.279 1 16.07 ? "H3'2" BNG 502 A 1 
HETATM 35 H "H4'1" BNG . . . D 3 13.758 -44.743 42.424 1 16.07 ? "H4'1" BNG 502 A 1 
HETATM 36 H "H4'2" BNG . . . D 3 14.536 -43.798 43.703 1 16.07 ? "H4'2" BNG 502 A 1 
HETATM 37 H "H5'1" BNG . . . D 3 16.159 -42.887 42.151 1 16.07 ? "H5'1" BNG 502 A 1 
HETATM 38 H "H5'2" BNG . . . D 3 15.292 -43.54 40.765 1 16.07 ? "H5'2" BNG 502 A 1 
HETATM 39 H "H6'1" BNG . . . D 3 15.788 -45.867 41.626 1 16.07 ? "H6'1" BNG 502 A 1 
HETATM 40 H "H6'2" BNG . . . D 3 16.786 -45.134 42.89 1 16.07 ? "H6'2" BNG 502 A 1 
HETATM 41 H "H7'1" BNG . . . D 3 18.214 -44.065 41.191 1 16.07 ? "H7'1" BNG 502 A 1 
HETATM 42 H "H7'2" BNG . . . D 3 17.18 -44.675 39.898 1 16.07 ? "H7'2" BNG 502 A 1 
HETATM 43 H "H8'1" BNG . . . D 3 17.717 -47.025 40.657 1 16.07 ? "H8'1" BNG 502 A 1 
HETATM 44 H "H8'2" BNG . . . D 3 18.858 -46.343 41.819 1 16.07 ? "H8'2" BNG 502 A 1 
HETATM 45 H "H9'1" BNG . . . D 3 19.993 -47.026 39.764 1 16.07 ? "H9'1" BNG 502 A 1 
HETATM 46 H "H9'2" BNG . . . D 3 20.102 -45.312 39.966 1 16.07 ? "H9'2" BNG 502 A 1 
HETATM 47 H "H9'3" BNG . . . D 3 18.984 -45.98 38.828 1 16.07 ? "H9'3" BNG 502 A 1 
HETATM 48 H HO2 BNG . . . D 3 8.059 -42.05 44.321 1 16.07 ? HO2 BNG 502 A 1 
HETATM 49 H HO3 BNG . . . D 3 5.794 -39.707 45.227 1 16.07 ? HO3 BNG 502 A 1 
HETATM 50 H HO4 BNG . . . D 3 7.67 -35.672 43.94 1 16.07 ? HO4 BNG 502 A 1 
HETATM 51 H HO6 BNG . . . D 3 12.077 -35.806 43.265 1 16.07 ? HO6 BNG 502 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           303 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           51 
#