data_4GBY # _model_server_result.job_id r8sHyT7vWu5yR7S8dYDybg _model_server_result.datetime_utc '2024-11-30 09:36:02' _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":"F","auth_seq_id":505}' # _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 . . . F 3 45.097 -10.392 -11.943 1 113.07 ? C1 BNG 505 A 1 HETATM 2 C C2 BNG . . . F 3 45.615 -9.352 -12.91 1 114.68 ? C2 BNG 505 A 1 HETATM 3 C C3 BNG . . . F 3 45.872 -8.017 -12.252 1 116.29 ? C3 BNG 505 A 1 HETATM 4 C C4 BNG . . . F 3 44.653 -7.61 -11.466 1 115.1 ? C4 BNG 505 A 1 HETATM 5 C C5 BNG . . . F 3 44.386 -8.691 -10.449 1 113.75 ? C5 BNG 505 A 1 HETATM 6 C C6 BNG . . . F 3 43.222 -8.292 -9.568 1 112.73 ? C6 BNG 505 A 1 HETATM 7 C C1' BNG . . . F 3 44.522 -12.677 -12.096 1 110.53 ? C1' BNG 505 A 1 HETATM 8 C C2' BNG . . . F 3 44.238 -13.78 -13.107 1 109.42 ? C2' BNG 505 A 1 HETATM 9 C C3' BNG . . . F 3 44.149 -15.133 -12.418 1 108.47 ? C3' BNG 505 A 1 HETATM 10 C C4' BNG . . . F 3 43.619 -16.196 -13.363 1 107.25 ? C4' BNG 505 A 1 HETATM 11 C C5' BNG . . . F 3 43.303 -17.471 -12.602 1 106.23 ? C5' BNG 505 A 1 HETATM 12 C C6' BNG . . . F 3 44.187 -18.613 -13.071 1 106.9 ? C6' BNG 505 A 1 HETATM 13 C C7' BNG . . . F 3 43.484 -19.957 -12.947 1 105.57 ? C7' BNG 505 A 1 HETATM 14 C C8' BNG . . . F 3 43.353 -20.624 -14.31 1 105.31 ? C8' BNG 505 A 1 HETATM 15 C C9' BNG . . . F 3 43.41 -22.127 -14.189 1 105.06 ? C9' BNG 505 A 1 HETATM 16 O O1 BNG . . . F 3 44.575 -11.424 -12.76 1 111.54 ? O1 BNG 505 A 1 HETATM 17 O O2 BNG . . . F 3 46.842 -9.835 -13.446 1 115.94 ? O2 BNG 505 A 1 HETATM 18 O O3 BNG . . . F 3 46.117 -7.055 -13.272 1 117.63 ? O3 BNG 505 A 1 HETATM 19 O O4 BNG . . . F 3 44.883 -6.368 -10.804 1 116.73 ? O4 BNG 505 A 1 HETATM 20 O O5 BNG . . . F 3 44.044 -9.876 -11.145 1 112.18 ? O5 BNG 505 A 1 HETATM 21 O O6 BNG . . . F 3 42.266 -9.344 -9.618 1 110.56 ? O6 BNG 505 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 222 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #