data_6VBG # _model_server_result.job_id 05R62AELPpDRz5Yf9inPgA _model_server_result.datetime_utc '2024-10-19 17:34:18' _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 6vbg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":702}' # _entry.id 6VBG # _exptl.entry_id 6VBG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.395 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'nonyl beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 9 _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 120 _cell.entry_id 6VBG _cell.length_a 151.27 _cell.length_b 151.27 _cell.length_c 182.48 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VBG _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall 'P 65' _symmetry.space_group_name_H-M 'P 65' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 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,B,E,G,H,I,J,P 1 1 C,D,F,K,L,M,N,O,Q 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 ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N N N ? 4 O N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 GAL _pdbx_entity_branch_link.comp_id_2 YIO _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 S1 _pdbx_entity_branch_link.leaving_atom_id_2 HS1 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n E YIO 1 E 1 YIO E 501 TDG 3 n E GAL 2 E 2 GAL E 501 TDG 3 n F YIO 1 F 1 YIO F 501 TDG 3 n F GAL 2 F 2 GAL F 501 TDG # 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 disulf ? disulf1 B SG CYS 22 C CYS 22 1_555 B SG CYS 96 C CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 D SG CYS 22 D CYS 22 1_555 D SG CYS 96 D CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 E S1 YIO . E YIO 1 1_555 E C1 GAL . E GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.796 sing covale ? covale2 F S1 YIO . F YIO 1 1_555 F C1 GAL . F GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.795 sing # _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 6VBG _atom_sites.fract_transf_matrix[1][1] 0.006611 _atom_sites.fract_transf_matrix[1][2] 0.003817 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007633 _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] 0.00548 _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 G 4 BNG A 1 701 701 BNG BNG . H 4 BNG A 1 702 901 BNG BNG . I 4 BNG C 1 501 501 BNG BNG . J 4 BNG C 1 502 601 BNG BNG . K 4 BNG B 1 801 801 BNG BNG . L 4 BNG B 1 802 501 BNG BNG . M 4 BNG B 1 803 701 BNG BNG . N 4 BNG B 1 804 801 BNG BNG . O 4 BNG D 1 601 601 BNG BNG . P 5 HOH A 1 801 1 HOH HOH . Q 5 HOH B 1 901 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 . . . H 4 -2.55 135.157 -40.269 1 129.23 ? C1 BNG 702 A 1 HETATM 2 C C2 BNG . . . H 4 -1.967 134.62 -41.566 1 129.26 ? C2 BNG 702 A 1 HETATM 3 C C3 BNG . . . H 4 -2.875 133.713 -42.301 1 124.61 ? C3 BNG 702 A 1 HETATM 4 C C4 BNG . . . H 4 -3.521 132.678 -41.443 1 100.37 ? C4 BNG 702 A 1 HETATM 5 C C5 BNG . . . H 4 -4.109 133.255 -40.156 1 89.91 ? C5 BNG 702 A 1 HETATM 6 C C6 BNG . . . H 4 -4.576 132.117 -39.301 1 107.34 ? C6 BNG 702 A 1 HETATM 7 C C1' BNG . . . H 4 -2 136.508 -38.468 1 96.52 ? C1' BNG 702 A 1 HETATM 8 C C2' BNG . . . H 4 -0.808 136.865 -37.57 1 85.93 ? C2' BNG 702 A 1 HETATM 9 C C3' BNG . . . H 4 -1.325 137.547 -36.299 1 88.34 ? C3' BNG 702 A 1 HETATM 10 C C4' BNG . . . H 4 -0.169 137.812 -35.326 1 86.98 ? C4' BNG 702 A 1 HETATM 11 C C5' BNG . . . H 4 -0.747 138.3 -33.985 1 88.9 ? C5' BNG 702 A 1 HETATM 12 C C6' BNG . . . H 4 0.202 139.318 -33.349 1 80.99 ? C6' BNG 702 A 1 HETATM 13 C C7' BNG . . . H 4 -0.282 139.657 -31.929 1 81.39 ? C7' BNG 702 A 1 HETATM 14 C C8' BNG . . . H 4 0.758 140.539 -31.227 1 95.1 ? C8' BNG 702 A 1 HETATM 15 C C9' BNG . . . H 4 0.515 140.523 -29.712 1 85.52 ? C9' BNG 702 A 1 HETATM 16 O O1 BNG . . . H 4 -1.553 135.766 -39.565 1 121.65 ? O1 BNG 702 A 1 HETATM 17 O O2 BNG . . . H 4 -1.675 135.749 -42.424 1 117.84 ? O2 BNG 702 A 1 HETATM 18 O O3 BNG . . . H 4 -2.083 133.012 -43.313 1 89.44 ? O3 BNG 702 A 1 HETATM 19 O O4 BNG . . . H 4 -4.59 132.07 -42.182 1 125.58 ? O4 BNG 702 A 1 HETATM 20 O O5 BNG . . . H 4 -3.121 134.055 -39.422 1 121.07 ? O5 BNG 702 A 1 HETATM 21 O O6 BNG . . . H 4 -3.473 131.43 -38.777 1 95.38 ? O6 BNG 702 A 1 HETATM 22 H H1 BNG . . . H 4 -3.247 135.8 -40.474 1 155.19 ? H1 BNG 702 A 1 HETATM 23 H H2 BNG . . . H 4 -1.161 134.126 -41.348 1 155.22 ? H2 BNG 702 A 1 HETATM 24 H H3 BNG . . . H 4 -3.573 134.253 -42.704 1 149.64 ? H3 BNG 702 A 1 HETATM 25 H H4 BNG . . . H 4 -2.851 132.015 -41.214 1 120.54 ? H4 BNG 702 A 1 HETATM 26 H H5 BNG . . . H 4 -4.869 133.821 -40.366 1 108 ? H5 BNG 702 A 1 HETATM 27 H H61 BNG . . . H 4 -5.109 131.509 -39.837 1 128.91 ? H61 BNG 702 A 1 HETATM 28 H H62 BNG . . . H 4 -5.115 132.463 -38.572 1 128.91 ? H62 BNG 702 A 1 HETATM 29 H "H1'1" BNG . . . H 4 -2.64 135.983 -37.963 1 115.93 ? "H1'1" BNG 702 A 1 HETATM 30 H "H1'2" BNG . . . H 4 -2.424 137.322 -38.781 1 115.93 ? "H1'2" BNG 702 A 1 HETATM 31 H "H2'1" BNG . . . H 4 -0.213 137.468 -38.043 1 103.22 ? "H2'1" BNG 702 A 1 HETATM 32 H "H2'2" BNG . . . H 4 -0.326 136.057 -37.332 1 103.22 ? "H2'2" BNG 702 A 1 HETATM 33 H "H3'1" BNG . . . H 4 -1.978 136.971 -35.871 1 106.11 ? "H3'1" BNG 702 A 1 HETATM 34 H "H3'2" BNG . . . H 4 -1.744 138.389 -36.536 1 106.11 ? "H3'2" BNG 702 A 1 HETATM 35 H "H4'1" BNG . . . H 4 0.417 138.491 -35.695 1 104.48 ? "H4'1" BNG 702 A 1 HETATM 36 H "H4'2" BNG . . . H 4 0.332 136.993 -35.186 1 104.48 ? "H4'2" BNG 702 A 1 HETATM 37 H "H5'1" BNG . . . H 4 -0.855 137.544 -33.387 1 106.78 ? "H5'1" BNG 702 A 1 HETATM 38 H "H5'2" BNG . . . H 4 -1.609 138.717 -34.139 1 106.78 ? "H5'2" BNG 702 A 1 HETATM 39 H "H6'1" BNG . . . H 4 0.217 140.125 -33.886 1 97.3 ? "H6'1" BNG 702 A 1 HETATM 40 H "H6'2" BNG . . . H 4 1.095 138.942 -33.304 1 97.3 ? "H6'2" BNG 702 A 1 HETATM 41 H "H7'1" BNG . . . H 4 -0.403 138.837 -31.425 1 97.78 ? "H7'1" BNG 702 A 1 HETATM 42 H "H7'2" BNG . . . H 4 -1.126 140.132 -31.981 1 97.78 ? "H7'2" BNG 702 A 1 HETATM 43 H "H8'1" BNG . . . H 4 0.683 141.449 -31.555 1 114.22 ? "H8'1" BNG 702 A 1 HETATM 44 H "H8'2" BNG . . . H 4 1.647 140.2 -31.414 1 114.22 ? "H8'2" BNG 702 A 1 HETATM 45 H "H9'1" BNG . . . H 4 1.197 141.052 -29.269 1 102.73 ? "H9'1" BNG 702 A 1 HETATM 46 H "H9'2" BNG . . . H 4 0.552 139.61 -29.388 1 102.73 ? "H9'2" BNG 702 A 1 HETATM 47 H "H9'3" BNG . . . H 4 -0.359 140.899 -29.521 1 102.73 ? "H9'3" BNG 702 A 1 HETATM 48 H HO2 BNG . . . H 4 -1.235 136.334 -41.993 1 141.52 ? HO2 BNG 702 A 1 HETATM 49 H HO3 BNG . . . H 4 -1.891 133.537 -43.951 1 107.43 ? HO3 BNG 702 A 1 HETATM 50 H HO4 BNG . . . H 4 -4.287 131.451 -42.679 1 150.8 ? HO4 BNG 702 A 1 HETATM 51 H HO6 BNG . . . H 4 -3.743 130.739 -38.361 1 114.56 ? HO6 BNG 702 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 51 #