data_6G9X # _model_server_result.job_id oFn4V5ENJtBQoMQnEDl9rg _model_server_result.datetime_utc '2024-11-02 21:35:33' _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 6g9x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":509}' # _entry.id 6G9X # _exptl.entry_id 6G9X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.395 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'nonyl beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 6 _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 6G9X _cell.length_a 106.765 _cell.length_b 200.539 _cell.length_c 64.561 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6G9X _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab' _symmetry.space_group_name_H-M 'P 21 21 2' # 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,E,F,G,H,I,J,K,L,M,N,X 1 1 B,O,P,Q,R,S,T,U,V,W,Y 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 ? 5 K N N ? 5 L N N ? 5 M N N ? 5 U N N ? 5 V N N ? 5 W 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 SG CYS 56 A CYS 56 1_555 D HG HG . A HG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc2 A SG CYS 57 A CYS 57 1_555 G HG HG . A HG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc3 A O CYS 362 A CYS 362 1_555 C HG HG . A HG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc4 A O GLY 366 A GLY 366 1_555 G HG HG . A HG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.022 ? metalc ? metalc5 A SG CYS 389 A CYS 389 1_555 E HG HG . A HG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc6 E HG HG . A HG 503 1_555 L O2 BNG . A BNG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.958 ? metalc ? metalc7 L O3 BNG . A BNG 510 1_555 N HG HG . A HG 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc8 B SG CYS 56 B CYS 56 1_555 P HG HG . B HG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc9 B SG CYS 57 B CYS 57 1_555 R HG HG . B HG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc10 B O CYS 362 B CYS 362 1_555 O HG HG . B HG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc11 B O GLY 366 B GLY 366 1_555 R HG HG . B HG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.099 ? metalc ? metalc12 B SG CYS 389 B CYS 389 1_555 Q HG HG . B HG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc13 B SG CYS 394 B CYS 394 1_555 S HG HG . B HG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? # _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 6G9X _atom_sites.fract_transf_matrix[1][1] 0.009366 _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] 0.004987 _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] 0.015489 _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 HG A 1 501 1 HG HG . D 2 HG A 1 502 3 HG HG . E 2 HG A 1 503 5 HG HG . F 2 HG A 1 504 7 HG HG . G 2 HG A 1 505 9 HG HG . H 2 HG A 1 506 12 HG HG . I 3 JKE A 1 507 1 JKE JKE . J 4 EPE A 1 508 1 EPE EPE . K 5 BNG A 1 509 3 BNG BNG . L 5 BNG A 1 510 4 BNG BNG . M 5 BNG A 1 511 6 BNG BNG . N 2 HG A 1 512 8 HG HG . O 2 HG B 1 501 2 HG HG . P 2 HG B 1 502 4 HG HG . Q 2 HG B 1 503 6 HG HG . R 2 HG B 1 504 10 HG HG . S 2 HG B 1 505 11 HG HG . T 3 JKE B 1 506 2 JKE JKE . U 5 BNG B 1 507 1 BNG BNG . V 5 BNG B 1 508 2 BNG BNG . W 5 BNG B 1 509 5 BNG BNG . X 6 HOH A 1 601 1 HOH HOH . Y 6 HOH B 1 601 2 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 . . . K 5 110.328 45.567 55.092 1 97.49 ? C1 BNG 509 A 1 HETATM 2 C C2 BNG . . . K 5 109.324 46.547 54.457 1 96.46 ? C2 BNG 509 A 1 HETATM 3 C C3 BNG . . . K 5 109.151 47.811 55.232 1 96.85 ? C3 BNG 509 A 1 HETATM 4 C C4 BNG . . . K 5 108.829 47.511 56.671 1 99.96 ? C4 BNG 509 A 1 HETATM 5 C C5 BNG . . . K 5 109.885 46.595 57.317 1 98.63 ? C5 BNG 509 A 1 HETATM 6 C C6 BNG . . . K 5 109.452 46.309 58.726 1 93.44 ? C6 BNG 509 A 1 HETATM 7 C C1' BNG . . . K 5 111.419 44.082 53.724 1 90.06 ? C1' BNG 509 A 1 HETATM 8 C C2' BNG . . . K 5 111.158 42.89 52.763 1 77.39 ? C2' BNG 509 A 1 HETATM 9 C C3' BNG . . . K 5 111.376 41.564 53.523 1 76.65 ? C3' BNG 509 A 1 HETATM 10 C C4' BNG . . . K 5 110.848 40.376 52.634 1 70.51 ? C4' BNG 509 A 1 HETATM 11 C C5' BNG . . . K 5 110.652 39.051 53.44 1 65.11 ? C5' BNG 509 A 1 HETATM 12 C C6' BNG . . . K 5 110.119 37.98 52.424 1 71.06 ? C6' BNG 509 A 1 HETATM 13 C C7' BNG . . . K 5 111.222 37.628 51.367 1 79.08 ? C7' BNG 509 A 1 HETATM 14 C C8' BNG . . . K 5 110.928 36.202 50.774 1 73.15 ? C8' BNG 509 A 1 HETATM 15 C C9' BNG . . . K 5 110.743 36.271 49.236 1 70.87 ? C9' BNG 509 A 1 HETATM 16 O O1 BNG . . . K 5 110.235 44.375 54.439 1 93.74 ? O1 BNG 509 A 1 HETATM 17 O O2 BNG . . . K 5 109.722 46.846 53.107 1 90.3 ? O2 BNG 509 A 1 HETATM 18 O O3 BNG . . . K 5 108.05 48.582 54.651 1 89.96 ? O3 BNG 509 A 1 HETATM 19 O O4 BNG . . . K 5 108.733 48.72 57.43 1 96.17 ? O4 BNG 509 A 1 HETATM 20 O O5 BNG . . . K 5 110.115 45.332 56.57 1 92.78 ? O5 BNG 509 A 1 HETATM 21 O O6 BNG . . . K 5 109.851 45.007 59.072 1 95.05 ? O6 BNG 509 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #