data_2YDO # _model_server_result.job_id i60Jyf0-EcYqC3Uhp-NpHg _model_server_result.datetime_utc '2024-11-28 10:28:21' _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 2ydo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 2YDO # _exptl.entry_id 2YDO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.434 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'octyl 1-thio-beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93.49 _cell.angle_gamma 90 _cell.entry_id 2YDO _cell.length_a 76.465 _cell.length_b 98.869 _cell.length_c 79.516 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YDO _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 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,D,E _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 ? 3 C N N ? 3 D 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 disulf ? disulf1 A SG CYS 71 A CYS 71 1_555 A SG CYS 159 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 74 A CYS 74 1_555 A SG CYS 146 A CYS 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf3 A SG CYS 77 A CYS 77 1_555 A SG CYS 166 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 259 A CYS 259 1_555 A SG CYS 262 A CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? # _chem_comp.formula 'C14 H28 O5 S' _chem_comp.formula_weight 308.434 _chem_comp.id SOG _chem_comp.mon_nstd_flag . _chem_comp.name 'octyl 1-thio-beta-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms '2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL;1-S-OCTYL-BETA-D-THIOGLUCOSIDE;octyl 1-thio-beta-D-glucoside;octyl 1-thio-D-glucoside;octyl 1-thio-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 SOG sing 324 n n C1 S1 SOG sing 325 n n C1 O5 SOG sing 326 n n C1 H1 SOG sing 327 n n C2 C3 SOG sing 328 n n C2 O2 SOG sing 329 n n C2 H2 SOG sing 330 n n C3 C4 SOG sing 331 n n C3 O3 SOG sing 332 n n C3 H3 SOG sing 333 n n C4 C5 SOG sing 334 n n C4 O4 SOG sing 335 n n C4 H4 SOG sing 336 n n C5 C6 SOG sing 337 n n C5 O5 SOG sing 338 n n C5 H5 SOG sing 339 n n C6 O6 SOG sing 340 n n C6 H61 SOG sing 341 n n C6 H62 SOG sing 342 n n C1' C2' SOG sing 343 n n C1' S1 SOG sing 344 n n C1' "H1'1" SOG sing 345 n n C1' "H1'2" SOG sing 346 n n C2' C3' SOG sing 347 n n C2' "H2'1" SOG sing 348 n n C2' "H2'2" SOG sing 349 n n C3' C4' SOG sing 350 n n C3' "H3'1" SOG sing 351 n n C3' "H3'2" SOG sing 352 n n C4' C5' SOG sing 353 n n C4' "H4'1" SOG sing 354 n n C4' "H4'2" SOG sing 355 n n C5' C6' SOG sing 356 n n C5' "H5'1" SOG sing 357 n n C5' "H5'2" SOG sing 358 n n C6' C7' SOG sing 359 n n C6' "H6'1" SOG sing 360 n n C6' "H6'2" SOG sing 361 n n C7' C8' SOG sing 362 n n C7' "H7'1" SOG sing 363 n n C7' "H7'2" SOG sing 364 n n C8' "H8'1" SOG sing 365 n n C8' "H8'2" SOG sing 366 n n C8' "H8'3" SOG sing 367 n n O2 HO2 SOG sing 368 n n O3 HO3 SOG sing 369 n n O4 HO4 SOG sing 370 n n O6 HO6 SOG sing 371 n n # _atom_sites.entry_id 2YDO _atom_sites.fract_transf_matrix[1][1] 0.013078 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000798 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010114 _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] 0.012599 _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 ADN A 1 400 400 ADN ADN . C 3 SOG A 1 501 501 SOG SOG . D 3 SOG A 1 502 502 SOG SOG . E 4 HOH A 1 2001 2001 HOH HOH . E 4 HOH A 2 2002 2002 HOH HOH . E 4 HOH A 3 2003 2003 HOH HOH . E 4 HOH A 4 2004 2004 HOH HOH . E 4 HOH A 5 2005 2005 HOH HOH . E 4 HOH A 6 2006 2006 HOH HOH . E 4 HOH A 7 2007 2007 HOH HOH . E 4 HOH A 8 2008 2008 HOH HOH . E 4 HOH A 9 2009 2009 HOH HOH . E 4 HOH A 10 2010 2010 HOH HOH . E 4 HOH A 11 2011 2011 HOH HOH . E 4 HOH A 12 2012 2012 HOH HOH . E 4 HOH A 13 2013 2013 HOH HOH . E 4 HOH A 14 2014 2014 HOH HOH . E 4 HOH A 15 2015 2015 HOH HOH . E 4 HOH A 16 2016 2016 HOH HOH . E 4 HOH A 17 2017 2017 HOH HOH . E 4 HOH A 18 2018 2018 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 SOG . . . C 3 -37.529 -1.211 -38.282 1 118.59 ? C1 SOG 501 A 1 HETATM 2 C C2 SOG . . . C 3 -36.39 -1.664 -37.366 1 116.7 ? C2 SOG 501 A 1 HETATM 3 C C3 SOG . . . C 3 -36.505 -3.141 -36.987 1 120.25 ? C3 SOG 501 A 1 HETATM 4 C C4 SOG . . . C 3 -37.934 -3.612 -36.689 1 124.55 ? C4 SOG 501 A 1 HETATM 5 C C5 SOG . . . C 3 -38.985 -2.96 -37.593 1 124.2 ? C5 SOG 501 A 1 HETATM 6 C C6 SOG . . . C 3 -40.406 -3.241 -37.105 1 123.51 ? C6 SOG 501 A 1 HETATM 7 C C1' SOG . . . C 3 -39.014 1.108 -38.121 1 106.52 ? C1' SOG 501 A 1 HETATM 8 C C2' SOG . . . C 3 -39.101 2.628 -38.209 1 100.04 ? C2' SOG 501 A 1 HETATM 9 C C3' SOG . . . C 3 -40.415 3.131 -37.616 1 95.14 ? C3' SOG 501 A 1 HETATM 10 C C4' SOG . . . C 3 -40.649 4.592 -37.981 1 92.84 ? C4' SOG 501 A 1 HETATM 11 C C5' SOG . . . C 3 -41.904 5.129 -37.306 1 95.18 ? C5' SOG 501 A 1 HETATM 12 C C6' SOG . . . C 3 -41.896 6.655 -37.28 1 95.04 ? C6' SOG 501 A 1 HETATM 13 C C7' SOG . . . C 3 -43.099 7.2 -36.516 1 92.44 ? C7' SOG 501 A 1 HETATM 14 C C8' SOG . . . C 3 -43.21 8.7 -36.684 1 90.78 ? C8' SOG 501 A 1 HETATM 15 S S1 SOG . . . C 3 -37.424 0.528 -38.633 1 115.86 ? S1 SOG 501 A 1 HETATM 16 O O2 SOG . . . C 3 -35.144 -1.487 -38.038 1 111.79 ? O2 SOG 501 A 1 HETATM 17 O O3 SOG . . . C 3 -35.686 -3.381 -35.835 1 121.37 ? O3 SOG 501 A 1 HETATM 18 O O4 SOG . . . C 3 -37.985 -5.035 -36.861 1 127.81 ? O4 SOG 501 A 1 HETATM 19 O O5 SOG . . . C 3 -38.772 -1.546 -37.658 1 122.98 ? O5 SOG 501 A 1 HETATM 20 O O6 SOG . . . C 3 -40.792 -2.288 -36.107 1 121.02 ? O6 SOG 501 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #