data_1VGO # _model_server_result.job_id Wmcl4QM6As_UMzrcmxzotQ _model_server_result.datetime_utc '2024-11-02 05:33:11' _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 1vgo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 1VGO # _exptl.entry_id 1VGO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.395 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'nonyl beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 12 _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 1VGO _cell.length_a 122.88 _cell.length_b 139.48 _cell.length_c 108.1 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VGO _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 N N N ? 2 O N N ? 2 P 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 covale ? covale1 A NZ LYS 221 A LYS 221 1_555 M C15 RET . A RET 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 ? covale ? covale2 B NZ LYS 221 B LYS 221 1_555 S C15 RET . B RET 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? # _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 1VGO _atom_sites.fract_transf_matrix[1][1] 0.008138 _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] 0.007169 _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] 0.009251 _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 BNG A 1 301 301 BNG BNG . D 2 BNG A 1 302 302 BNG BNG . E 2 BNG A 1 303 303 BNG BNG . F 2 BNG A 1 304 304 BNG BNG . G 2 BNG A 1 305 305 BNG BNG . H 2 BNG A 1 306 306 BNG BNG . I 2 BNG A 1 307 307 BNG BNG . J 2 BNG A 1 308 308 BNG BNG . K 2 BNG A 1 309 309 BNG BNG . L 3 SO4 A 1 400 400 SO4 SO4 . M 4 RET A 1 260 260 RET RET . N 2 BNG B 1 310 310 BNG BNG . O 2 BNG B 1 311 311 BNG BNG . P 2 BNG B 1 312 312 BNG BNG . Q 3 SO4 B 1 401 401 SO4 SO4 . R 3 SO4 B 1 402 402 SO4 SO4 . S 4 RET B 1 261 261 RET RET . T 5 HOH A 1 501 501 HOH HOH . T 5 HOH A 2 502 502 HOH HOH . T 5 HOH A 3 503 503 HOH HOH . T 5 HOH A 4 504 504 HOH HOH . T 5 HOH A 5 505 505 HOH HOH . T 5 HOH A 6 506 506 HOH HOH . T 5 HOH A 7 507 507 HOH HOH . T 5 HOH A 8 508 508 HOH HOH . T 5 HOH A 9 509 509 HOH HOH . T 5 HOH A 10 510 510 HOH HOH . T 5 HOH A 11 511 511 HOH HOH . T 5 HOH A 12 512 512 HOH HOH . T 5 HOH A 13 513 513 HOH HOH . T 5 HOH A 14 701 701 HOH HOH . T 5 HOH A 15 702 702 HOH HOH . T 5 HOH A 16 705 705 HOH HOH . U 5 HOH B 1 601 601 HOH HOH . U 5 HOH B 2 602 602 HOH HOH . U 5 HOH B 3 603 603 HOH HOH . U 5 HOH B 4 605 605 HOH HOH . U 5 HOH B 5 606 606 HOH HOH . U 5 HOH B 6 607 607 HOH HOH . U 5 HOH B 7 608 608 HOH HOH . U 5 HOH B 8 700 700 HOH HOH . U 5 HOH B 9 703 703 HOH HOH . U 5 HOH B 10 704 704 HOH HOH . U 5 HOH B 11 706 706 HOH HOH . U 5 HOH B 12 707 707 HOH HOH . U 5 HOH B 13 708 708 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 . . . C 2 7.35 -2.217 68.556 1 77.22 ? C1 BNG 301 A 1 HETATM 2 C C2 BNG . . . C 2 7.941 -3.127 69.727 1 77.45 ? C2 BNG 301 A 1 HETATM 3 C C3 BNG . . . C 2 7.056 -2.924 71.022 1 77.83 ? C3 BNG 301 A 1 HETATM 4 C C4 BNG . . . C 2 7.134 -1.453 71.416 1 78.88 ? C4 BNG 301 A 1 HETATM 5 C C5 BNG . . . C 2 6.581 -0.556 70.226 1 78.73 ? C5 BNG 301 A 1 HETATM 6 C C6 BNG . . . C 2 6.696 0.911 70.642 1 79.46 ? C6 BNG 301 A 1 HETATM 7 C C1' BNG . . . C 2 7.557 -1.997 66.176 1 76.42 ? C1' BNG 301 A 1 HETATM 8 C C2' BNG . . . C 2 8.49 -2.207 64.939 1 74.23 ? C2' BNG 301 A 1 HETATM 9 C C3' BNG . . . C 2 7.838 -1.775 63.666 1 75.36 ? C3' BNG 301 A 1 HETATM 10 C C4' BNG . . . C 2 8.836 -1.762 62.48 1 75.85 ? C4' BNG 301 A 1 HETATM 11 C C5' BNG . . . C 2 8.162 -1.337 61.201 1 74.94 ? C5' BNG 301 A 1 HETATM 12 C C6' BNG . . . C 2 8.18 -2.491 60.178 1 77.21 ? C6' BNG 301 A 1 HETATM 13 C C7' BNG . . . C 2 7.517 -2.144 58.854 1 78.08 ? C7' BNG 301 A 1 HETATM 14 C C8' BNG . . . C 2 7.568 -3.359 57.88 1 77.05 ? C8' BNG 301 A 1 HETATM 15 C C9' BNG . . . C 2 6.913 -3.027 56.569 1 76.62 ? C9' BNG 301 A 1 HETATM 16 O O1 BNG . . . C 2 8.191 -2.411 67.365 1 76.52 ? O1 BNG 301 A 1 HETATM 17 O O2 BNG . . . C 2 7.898 -4.486 69.331 1 76.63 ? O2 BNG 301 A 1 HETATM 18 O O3 BNG . . . C 2 7.569 -3.731 72.1 1 76.79 ? O3 BNG 301 A 1 HETATM 19 O O4 BNG . . . C 2 6.331 -1.216 72.624 1 78.2 ? O4 BNG 301 A 1 HETATM 20 O O5 BNG . . . C 2 7.397 -0.83 69.01 1 79.27 ? O5 BNG 301 A 1 HETATM 21 O O6 BNG . . . C 2 6.25 1.834 69.675 1 84.27 ? O6 BNG 301 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 212 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #