data_6FVR # _model_server_result.job_id b2jhU5Ug76_gvhkXo3V3qg _model_server_result.datetime_utc '2024-10-20 12:46:30' _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 6fvr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":401}' # _entry.id 6FVR # _exptl.entry_id 6FVR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.395 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'nonyl beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 111.75 _cell.angle_gamma 90 _cell.entry_id 6FVR _cell.length_a 221.169 _cell.length_b 114.107 _cell.length_c 144.274 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6FVR _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,H,I,J,K,L,M,N,O,P,Q,R,S,T,U _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 ? 2 F N N ? 2 H N N ? 2 L N N ? 2 O N N ? 2 R N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A O PHE 78 A PHE 78 1_555 G CS CS . A CS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.024 ? metalc ? metalc2 B O GLU 27 B GLU 27 1_555 I CS CS . B CS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.326 ? metalc ? metalc3 B O PHE 78 B PHE 78 1_555 K CS CS . B CS 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? metalc ? metalc4 B O GLY 158 B GLY 158 1_555 J CS CS . B CS 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.426 ? metalc ? metalc5 B OE1 GLU 159 B GLU 159 1_555 J CS CS . B CS 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.134 ? metalc ? metalc6 C O PHE 78 C PHE 78 1_555 M CS CS . C CS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.982 ? metalc ? metalc7 C O GLY 158 C GLY 158 1_555 N CS CS . C CS 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.168 ? metalc ? metalc8 N CS CS . C CS 403 1_555 D O GLU 27 D GLU 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.478 ? metalc ? metalc9 D O GLY 158 D GLY 158 1_555 Q CS CS . D CS 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.343 ? metalc ? metalc10 D OE1 GLU 159 D GLU 159 1_555 Q CS CS . D CS 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.356 ? metalc ? metalc11 E O PHE 78 E PHE 78 1_555 T CS CS . E CS 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.356 ? metalc ? metalc12 E OE1 GLU 159 E GLU 159 1_555 S CS CS . E CS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.382 ? # _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 6FVR _atom_sites.fract_transf_matrix[1][1] 0.004521 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001804 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008764 _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] 0.007463 _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 F 2 BNG A 1 401 319 BNG BNG . G 3 CS A 1 402 5 CS CS . H 2 BNG B 1 401 320 BNG BNG . I 3 CS B 1 402 1 CS CS . J 3 CS B 1 403 3 CS CS . K 3 CS B 1 404 4 CS CS . L 2 BNG C 1 401 321 BNG BNG . M 3 CS C 1 402 8 CS CS . N 3 CS C 1 403 9 CS CS . O 2 BNG D 1 401 322 BNG BNG . P 3 CS D 1 402 7 CS CS . Q 3 CS D 1 403 10 CS CS . R 2 BNG E 1 401 318 BNG BNG . S 3 CS E 1 402 2 CS CS . T 3 CS E 1 403 6 CS CS . U 3 CS E 1 404 11 CS CS . # 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 . . . R 2 -23.532 2.309 8.043 1 107.56 ? C1 BNG 401 E 1 HETATM 2 C C2 BNG . . . R 2 -22.87 1.701 9.279 1 110.48 ? C2 BNG 401 E 1 HETATM 3 C C3 BNG . . . R 2 -22.935 0.172 9.234 1 112.86 ? C3 BNG 401 E 1 HETATM 4 C C4 BNG . . . R 2 -24.332 -0.341 8.884 1 112.93 ? C4 BNG 401 E 1 HETATM 5 C C5 BNG . . . R 2 -24.884 0.405 7.668 1 110.95 ? C5 BNG 401 E 1 HETATM 6 C C6 BNG . . . R 2 -26.308 0.057 7.299 1 109.33 ? C6 BNG 401 E 1 HETATM 7 C C1' BNG . . . R 2 -23.973 4.397 7.004 1 92.12 ? C1' BNG 401 E 1 HETATM 8 C C2' BNG . . . R 2 -22.845 4.599 6.026 1 84.94 ? C2' BNG 401 E 1 HETATM 9 C C3' BNG . . . R 2 -23.106 5.689 5.002 1 74.7 ? C3' BNG 401 E 1 HETATM 10 C C4' BNG . . . R 2 -23.979 5.306 3.825 1 65.74 ? C4' BNG 401 E 1 HETATM 11 C C5' BNG . . . R 2 -25.269 6.096 3.686 1 59.4 ? C5' BNG 401 E 1 HETATM 12 C C6' BNG . . . R 2 -26.524 5.28 3.943 1 54.78 ? C6' BNG 401 E 1 HETATM 13 C C7' BNG . . . R 2 -27.015 5.365 5.372 1 51.24 ? C7' BNG 401 E 1 HETATM 14 C C8' BNG . . . R 2 -27.875 4.219 5.8 1 48.82 ? C8' BNG 401 E 1 HETATM 15 C C9' BNG . . . R 2 -27.502 3.743 7.134 1 47.85 ? C9' BNG 401 E 1 HETATM 16 O O1 BNG . . . R 2 -23.532 3.701 8.172 1 100.61 ? O1 BNG 401 E 1 HETATM 17 O O2 BNG . . . R 2 -21.507 2.113 9.341 1 110.01 ? O2 BNG 401 E 1 HETATM 18 O O3 BNG . . . R 2 -22.507 -0.382 10.475 1 114.06 ? O3 BNG 401 E 1 HETATM 19 O O4 BNG . . . R 2 -24.253 -1.735 8.599 1 113.29 ? O4 BNG 401 E 1 HETATM 20 O O5 BNG . . . R 2 -24.852 1.821 7.903 1 109.86 ? O5 BNG 401 E 1 HETATM 21 O O6 BNG . . . R 2 -27.257 0.551 8.236 1 108.45 ? O6 BNG 401 E 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #