data_3ODY # _model_server_result.job_id -b92rnm675umxfr1SzDKnw _model_server_result.datetime_utc '2024-11-25 02:36:50' _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 3ody # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1000}' # _entry.id 3ODY # _exptl.entry_id 3ODY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 292.369 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'octyl beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 95.24 _cell.angle_gamma 90 _cell.entry_id 3ODY _cell.length_a 37.9 _cell.length_b 71.815 _cell.length_c 63.542 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ODY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C14 H28 O6' _chem_comp.formula_weight 292.369 _chem_comp.id BOG _chem_comp.mon_nstd_flag n _chem_comp.name 'octyl beta-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'Beta-Octylglucoside;octyl beta-D-glucoside;octyl D-glucoside;octyl 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 O1 BOG sing 70 n n C1 C2 BOG sing 71 n n C1 O5 BOG sing 72 n n C1 H1 BOG sing 73 n n O1 C1' BOG sing 74 n n C2 O2 BOG sing 75 n n C2 C3 BOG sing 76 n n C2 H2 BOG sing 77 n n O2 HO2 BOG sing 78 n n C3 O3 BOG sing 79 n n C3 C4 BOG sing 80 n n C3 H3 BOG sing 81 n n O3 HO3 BOG sing 82 n n C4 O4 BOG sing 83 n n C4 C5 BOG sing 84 n n C4 H4 BOG sing 85 n n O4 HO4 BOG sing 86 n n C5 O5 BOG sing 87 n n C5 C6 BOG sing 88 n n C5 H5 BOG sing 89 n n C6 O6 BOG sing 90 n n C6 H61 BOG sing 91 n n C6 H62 BOG sing 92 n n O6 HO6 BOG sing 93 n n C1' C2' BOG sing 94 n n C1' "H1'1" BOG sing 95 n n C1' "H1'2" BOG sing 96 n n C2' C3' BOG sing 97 n n C2' "H2'1" BOG sing 98 n n C2' "H2'2" BOG sing 99 n n C3' C4' BOG sing 100 n n C3' "H3'1" BOG sing 101 n n C3' "H3'2" BOG sing 102 n n C4' C5' BOG sing 103 n n C4' "H4'1" BOG sing 104 n n C4' "H4'2" BOG sing 105 n n C5' C6' BOG sing 106 n n C5' "H5'1" BOG sing 107 n n C5' "H5'2" BOG sing 108 n n C6' C7' BOG sing 109 n n C6' "H6'1" BOG sing 110 n n C6' "H6'2" BOG sing 111 n n C7' C8' BOG sing 112 n n C7' "H7'1" BOG sing 113 n n C7' "H7'2" BOG sing 114 n n C8' "H8'1" BOG sing 115 n n C8' "H8'2" BOG sing 116 n n C8' "H8'3" BOG sing 117 n n # _pdbx_chem_comp_identifier.comp_id BOG _pdbx_chem_comp_identifier.identifier b-octylglucoside _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 3ODY _atom_sites.fract_transf_matrix[1][1] 0.026385 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002422 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013925 _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] 0.015804 _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 B 2 BOG X 1 1000 1000 BOG BOG . C 3 HOH X 1 361 1 HOH HOH . C 3 HOH X 2 362 2 HOH HOH . C 3 HOH X 3 363 3 HOH HOH . C 3 HOH X 4 364 4 HOH HOH . C 3 HOH X 5 365 6 HOH HOH . C 3 HOH X 6 366 7 HOH HOH . C 3 HOH X 7 367 8 HOH HOH . C 3 HOH X 8 368 9 HOH HOH . C 3 HOH X 9 369 11 HOH HOH . C 3 HOH X 10 370 12 HOH HOH . C 3 HOH X 11 371 14 HOH HOH . C 3 HOH X 12 372 17 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 BOG . . . B 2 7.937 -20.953 16.848 1 68.01 ? C1 BOG 1000 X 1 HETATM 2 O O1 BOG . . . B 2 8.771 -20.75 15.721 1 68.64 ? O1 BOG 1000 X 1 HETATM 3 C C2 BOG . . . B 2 8.759 -21.629 17.933 1 75.88 ? C2 BOG 1000 X 1 HETATM 4 O O2 BOG . . . B 2 9.224 -22.857 17.494 1 78.35 ? O2 BOG 1000 X 1 HETATM 5 C C3 BOG . . . B 2 7.966 -21.748 19.122 1 75.37 ? C3 BOG 1000 X 1 HETATM 6 O O3 BOG . . . B 2 8.63 -22.604 20.124 1 74.5 ? O3 BOG 1000 X 1 HETATM 7 C C4 BOG . . . B 2 7.74 -20.452 19.643 1 76.59 ? C4 BOG 1000 X 1 HETATM 8 O O4 BOG . . . B 2 7.008 -20.497 20.848 1 68.28 ? O4 BOG 1000 X 1 HETATM 9 C C5 BOG . . . B 2 6.994 -19.61 18.63 1 78.8 ? C5 BOG 1000 X 1 HETATM 10 O O5 BOG . . . B 2 7.499 -19.704 17.268 1 65.4 ? O5 BOG 1000 X 1 HETATM 11 C C6 BOG . . . B 2 6.985 -18.19 19.076 1 83.96 ? C6 BOG 1000 X 1 HETATM 12 O O6 BOG . . . B 2 8.068 -17.371 18.696 1 88.01 ? O6 BOG 1000 X 1 HETATM 13 C C1' BOG . . . B 2 8.538 -19.629 14.895 1 60.29 ? C1' BOG 1000 X 1 HETATM 14 C C2' BOG . . . B 2 7.776 -19.829 13.598 1 55.91 ? C2' BOG 1000 X 1 HETATM 15 C C3' BOG . . . B 2 7.394 -21.25 13.178 1 47.73 ? C3' BOG 1000 X 1 HETATM 16 C C4' BOG . . . B 2 6.919 -21.428 11.751 1 51.69 ? C4' BOG 1000 X 1 HETATM 17 C C5' BOG . . . B 2 6.408 -20.188 11.028 1 52.36 ? C5' BOG 1000 X 1 HETATM 18 C C6' BOG . . . B 2 5.346 -20.393 9.982 1 58.87 ? C6' BOG 1000 X 1 HETATM 19 C C7' BOG . . . B 2 5.604 -21.463 8.864 1 50.68 ? C7' BOG 1000 X 1 HETATM 20 C C8' BOG . . . B 2 4.515 -21.725 7.868 1 56.19 ? C8' BOG 1000 X 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #