data_6VBG # _model_server_result.job_id p2MO7vGPrg9AAjbM2D3qdQ _model_server_result.datetime_utc '2024-10-19 17:45:36' _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":"I","auth_seq_id":501}' # _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 . . . I 4 11.192 172.019 -24.986 1 135.08 ? C1 BNG 501 C 1 HETATM 2 C C2 BNG . . . I 4 12.523 172.558 -24.461 1 135.9 ? C2 BNG 501 C 1 HETATM 3 C C3 BNG . . . I 4 12.397 173.712 -23.541 1 124.88 ? C3 BNG 501 C 1 HETATM 4 C C4 BNG . . . I 4 11.46 174.76 -24.047 1 135.02 ? C4 BNG 501 C 1 HETATM 5 C C5 BNG . . . I 4 10.107 174.16 -24.422 1 144.13 ? C5 BNG 501 C 1 HETATM 6 C C6 BNG . . . I 4 9.228 175.229 -24.987 1 132.58 ? C6 BNG 501 C 1 HETATM 7 C C1' BNG . . . I 4 10.562 171.017 -27.017 1 127.18 ? C1' BNG 501 C 1 HETATM 8 C C2' BNG . . . I 4 11.126 171.542 -28.344 1 114.5 ? C2' BNG 501 C 1 HETATM 9 C C3' BNG . . . I 4 10.59 170.698 -29.504 1 116.06 ? C3' BNG 501 C 1 HETATM 10 C C4' BNG . . . I 4 11.364 169.374 -29.577 1 108.64 ? C4' BNG 501 C 1 HETATM 11 C C5' BNG . . . I 4 10.964 168.637 -30.867 1 97.71 ? C5' BNG 501 C 1 HETATM 12 C C6' BNG . . . I 4 10.981 167.124 -30.652 1 75.81 ? C6' BNG 501 C 1 HETATM 13 C C7' BNG . . . I 4 9.742 166.482 -31.3 1 81.53 ? C7' BNG 501 C 1 HETATM 14 C C8' BNG . . . I 4 9.259 165.306 -30.441 1 97.1 ? C8' BNG 501 C 1 HETATM 15 C C9' BNG . . . I 4 8.344 164.404 -31.278 1 87.96 ? C9' BNG 501 C 1 HETATM 16 O O1 BNG . . . I 4 11.529 171.196 -26.028 1 121.13 ? O1 BNG 501 C 1 HETATM 17 O O2 BNG . . . I 4 13.23 171.501 -23.767 1 105.03 ? O2 BNG 501 C 1 HETATM 18 O O3 BNG . . . I 4 13.718 174.31 -23.397 1 98.35 ? O3 BNG 501 C 1 HETATM 19 O O4 BNG . . . I 4 11.265 175.738 -23.026 1 137.73 ? O4 BNG 501 C 1 HETATM 20 O O5 BNG . . . I 4 10.268 173.104 -25.434 1 152.73 ? O5 BNG 501 C 1 HETATM 21 O O6 BNG . . . I 4 8.083 174.641 -25.542 1 131.56 ? O6 BNG 501 C 1 HETATM 22 H H1 BNG . . . I 4 10.708 171.526 -24.305 1 162.2 ? H1 BNG 501 C 1 HETATM 23 H H2 BNG . . . I 4 13.03 172.848 -25.236 1 163.18 ? H2 BNG 501 C 1 HETATM 24 H H3 BNG . . . I 4 12.068 173.398 -22.684 1 149.97 ? H3 BNG 501 C 1 HETATM 25 H H4 BNG . . . I 4 11.848 175.191 -24.824 1 162.13 ? H4 BNG 501 C 1 HETATM 26 H H5 BNG . . . I 4 9.685 173.8 -23.627 1 173.06 ? H5 BNG 501 C 1 HETATM 27 H H61 BNG . . . I 4 9.709 175.715 -25.675 1 159.2 ? H61 BNG 501 C 1 HETATM 28 H H62 BNG . . . I 4 8.968 175.841 -24.281 1 159.2 ? H62 BNG 501 C 1 HETATM 29 H "H1'1" BNG . . . I 4 9.76 171.51 -26.783 1 152.72 ? "H1'1" BNG 501 C 1 HETATM 30 H "H1'2" BNG . . . I 4 10.349 170.074 -27.1 1 152.72 ? "H1'2" BNG 501 C 1 HETATM 31 H "H2'1" BNG . . . I 4 12.094 171.487 -28.327 1 137.5 ? "H2'1" BNG 501 C 1 HETATM 32 H "H2'2" BNG . . . I 4 10.856 172.465 -28.467 1 137.5 ? "H2'2" BNG 501 C 1 HETATM 33 H "H3'1" BNG . . . I 4 10.702 171.184 -30.335 1 139.38 ? "H3'1" BNG 501 C 1 HETATM 34 H "H3'2" BNG . . . I 4 9.649 170.514 -29.361 1 139.38 ? "H3'2" BNG 501 C 1 HETATM 35 H "H4'1" BNG . . . I 4 11.146 168.826 -28.807 1 130.47 ? "H4'1" BNG 501 C 1 HETATM 36 H "H4'2" BNG . . . I 4 12.317 169.554 -29.586 1 130.47 ? "H4'2" BNG 501 C 1 HETATM 37 H "H5'1" BNG . . . I 4 11.59 168.865 -31.572 1 117.36 ? "H5'1" BNG 501 C 1 HETATM 38 H "H5'2" BNG . . . I 4 10.071 168.912 -31.127 1 117.36 ? "H5'2" BNG 501 C 1 HETATM 39 H "H6'1" BNG . . . I 4 10.979 166.935 -29.701 1 91.08 ? "H6'1" BNG 501 C 1 HETATM 40 H "H6'2" BNG . . . I 4 11.781 166.752 -31.054 1 91.08 ? "H6'2" BNG 501 C 1 HETATM 41 H "H7'1" BNG . . . I 4 9.972 166.161 -32.186 1 97.94 ? "H7'1" BNG 501 C 1 HETATM 42 H "H7'2" BNG . . . I 4 9.035 167.143 -31.368 1 97.94 ? "H7'2" BNG 501 C 1 HETATM 43 H "H8'1" BNG . . . I 4 8.768 165.644 -29.676 1 116.63 ? "H8'1" BNG 501 C 1 HETATM 44 H "H8'2" BNG . . . I 4 10.024 164.794 -30.134 1 116.63 ? "H8'2" BNG 501 C 1 HETATM 45 H "H9'1" BNG . . . I 4 8.209 163.562 -30.817 1 105.65 ? "H9'1" BNG 501 C 1 HETATM 46 H "H9'2" BNG . . . I 4 8.754 164.238 -32.141 1 105.65 ? "H9'2" BNG 501 C 1 HETATM 47 H "H9'3" BNG . . . I 4 7.488 164.842 -31.407 1 105.65 ? "H9'3" BNG 501 C 1 HETATM 48 H HO2 BNG . . . I 4 13.626 170.999 -24.328 1 126.14 ? HO2 BNG 501 C 1 HETATM 49 H HO3 BNG . . . I 4 14.307 173.699 -23.325 1 118.12 ? HO3 BNG 501 C 1 HETATM 50 H HO4 BNG . . . I 4 12.02 176.039 -22.779 1 165.38 ? HO4 BNG 501 C 1 HETATM 51 H HO6 BNG . . . I 4 7.568 175.25 -25.835 1 157.97 ? HO6 BNG 501 C 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 51 #