data_4GBY # _model_server_result.job_id UZN7RASncufZ2qYrfTzaSg _model_server_result.datetime_utc '2024-11-02 03:31:28' _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 4gby # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 4GBY # _exptl.entry_id 4GBY _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 4 _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 4GBY _cell.length_a 95.29 _cell.length_b 95.29 _cell.length_c 168.181 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GBY _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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,E,F,G _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E 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 70 n n C1 O1 BNG sing 71 n n C1 O5 BNG sing 72 n n C1 H1 BNG sing 73 n n C2 C3 BNG sing 74 n n C2 O2 BNG sing 75 n n C2 H2 BNG sing 76 n n C3 C4 BNG sing 77 n n C3 O3 BNG sing 78 n n C3 H3 BNG sing 79 n n C4 C5 BNG sing 80 n n C4 O4 BNG sing 81 n n C4 H4 BNG sing 82 n n C5 C6 BNG sing 83 n n C5 O5 BNG sing 84 n n C5 H5 BNG sing 85 n n C6 O6 BNG sing 86 n n C6 H61 BNG sing 87 n n C6 H62 BNG sing 88 n n C1' C2' BNG sing 89 n n C1' O1 BNG sing 90 n n C1' "H1'1" BNG sing 91 n n C1' "H1'2" BNG sing 92 n n C2' C3' BNG sing 93 n n C2' "H2'1" BNG sing 94 n n C2' "H2'2" BNG sing 95 n n C3' C4' BNG sing 96 n n C3' "H3'1" BNG sing 97 n n C3' "H3'2" BNG sing 98 n n C4' C5' BNG sing 99 n n C4' "H4'1" BNG sing 100 n n C4' "H4'2" BNG sing 101 n n C5' C6' BNG sing 102 n n C5' "H5'1" BNG sing 103 n n C5' "H5'2" BNG sing 104 n n C6' C7' BNG sing 105 n n C6' "H6'1" BNG sing 106 n n C6' "H6'2" BNG sing 107 n n C7' C8' BNG sing 108 n n C7' "H7'1" BNG sing 109 n n C7' "H7'2" BNG sing 110 n n C8' C9' BNG sing 111 n n C8' "H8'1" BNG sing 112 n n C8' "H8'2" BNG sing 113 n n C9' "H9'1" BNG sing 114 n n C9' "H9'2" BNG sing 115 n n C9' "H9'3" BNG sing 116 n n O2 HO2 BNG sing 117 n n O3 HO3 BNG sing 118 n n O4 HO4 BNG sing 119 n n O6 HO6 BNG sing 120 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 4GBY _atom_sites.fract_transf_matrix[1][1] 0.010494 _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] 0.010494 _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] 0.005946 _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 XYP A 1 501 1 XYP DXY . C 3 BNG A 1 502 1 BNG BNG . D 3 BNG A 1 503 2 BNG BNG . E 3 BNG A 1 504 3 BNG BNG . F 3 BNG A 1 505 4 BNG BNG . G 4 HOH A 1 601 1 HOH HOH . G 4 HOH A 2 602 2 HOH HOH . G 4 HOH A 3 603 3 HOH HOH . G 4 HOH A 4 604 4 HOH HOH . G 4 HOH A 5 605 5 HOH HOH . G 4 HOH A 6 606 6 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 BNG . . . D 3 -4.325 -7.957 -10.027 1 142.62 ? C1 BNG 503 A 1 HETATM 2 C C2 BNG . . . D 3 -5.236 -8.788 -9.153 1 142.46 ? C2 BNG 503 A 1 HETATM 3 C C3 BNG . . . D 3 -4.994 -8.447 -7.7 1 142.25 ? C3 BNG 503 A 1 HETATM 4 C C4 BNG . . . D 3 -3.524 -8.581 -7.361 1 140.68 ? C4 BNG 503 A 1 HETATM 5 C C5 BNG . . . D 3 -2.735 -7.789 -8.367 1 140.93 ? C5 BNG 503 A 1 HETATM 6 C C6 BNG . . . D 3 -1.253 -7.853 -8.087 1 139.56 ? C6 BNG 503 A 1 HETATM 7 C C1' BNG . . . D 3 -3.266 -8.4 -12.069 1 141.84 ? C1' BNG 503 A 1 HETATM 8 C C2' BNG . . . D 3 -3.391 -9.331 -13.27 1 141.54 ? C2' BNG 503 A 1 HETATM 9 C C3' BNG . . . D 3 -2.013 -9.713 -13.791 1 140.14 ? C3' BNG 503 A 1 HETATM 10 C C4' BNG . . . D 3 -2.116 -10.75 -14.905 1 139.83 ? C4' BNG 503 A 1 HETATM 11 C C5' BNG . . . D 3 -0.834 -10.83 -15.729 1 139.07 ? C5' BNG 503 A 1 HETATM 12 C C6' BNG . . . D 3 -0.173 -12.197 -15.593 1 137.32 ? C6' BNG 503 A 1 HETATM 13 C C7' BNG . . . D 3 -0.499 -13.09 -16.782 1 137.56 ? C7' BNG 503 A 1 HETATM 14 C C8' BNG . . . D 3 -1.731 -13.933 -16.494 1 137.87 ? C8' BNG 503 A 1 HETATM 15 C C9' BNG . . . D 3 -1.711 -15.196 -17.321 1 137.52 ? C9' BNG 503 A 1 HETATM 16 O O1 BNG . . . D 3 -4.518 -8.282 -11.392 1 142.92 ? O1 BNG 503 A 1 HETATM 17 O O2 BNG . . . D 3 -6.58 -8.462 -9.475 1 144.25 ? O2 BNG 503 A 1 HETATM 18 O O3 BNG . . . D 3 -5.796 -9.296 -6.89 1 142.1 ? O3 BNG 503 A 1 HETATM 19 O O4 BNG . . . D 3 -3.236 -7.956 -6.123 1 140.9 ? O4 BNG 503 A 1 HETATM 20 O O5 BNG . . . D 3 -2.993 -8.274 -9.67 1 140.96 ? O5 BNG 503 A 1 HETATM 21 O O6 BNG . . . D 3 -0.675 -6.735 -8.753 1 140.41 ? O6 BNG 503 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #