data_2YCZ # _model_server_result.job_id Xe-4n_s2VjDi8Qk06RBjqg _model_server_result.datetime_utc '2024-11-23 02:37:28' _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 2ycz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1360}' # _entry.id 2YCZ # _exptl.entry_id 2YCZ _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 116.39 _cell.angle_gamma 90 _cell.entry_id 2YCZ _cell.length_a 177.855 _cell.length_b 56.298 _cell.length_c 110.939 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YCZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C 1 1 B,D,E 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 84 A CYS 114 1_555 A SG CYS 169 A CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 A SG CYS 162 A CYS 192 1_555 A SG CYS 168 A CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? disulf ? disulf3 B SG CYS 84 B CYS 114 1_555 B SG CYS 169 B CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf4 B SG CYS 162 B CYS 192 1_555 B SG CYS 168 B CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? # _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 331 n n C1 S1 SOG sing 332 n n C1 O5 SOG sing 333 n n C1 H1 SOG sing 334 n n C2 C3 SOG sing 335 n n C2 O2 SOG sing 336 n n C2 H2 SOG sing 337 n n C3 C4 SOG sing 338 n n C3 O3 SOG sing 339 n n C3 H3 SOG sing 340 n n C4 C5 SOG sing 341 n n C4 O4 SOG sing 342 n n C4 H4 SOG sing 343 n n C5 C6 SOG sing 344 n n C5 O5 SOG sing 345 n n C5 H5 SOG sing 346 n n C6 O6 SOG sing 347 n n C6 H61 SOG sing 348 n n C6 H62 SOG sing 349 n n C1' C2' SOG sing 350 n n C1' S1 SOG sing 351 n n C1' "H1'1" SOG sing 352 n n C1' "H1'2" SOG sing 353 n n C2' C3' SOG sing 354 n n C2' "H2'1" SOG sing 355 n n C2' "H2'2" SOG sing 356 n n C3' C4' SOG sing 357 n n C3' "H3'1" SOG sing 358 n n C3' "H3'2" SOG sing 359 n n C4' C5' SOG sing 360 n n C4' "H4'1" SOG sing 361 n n C4' "H4'2" SOG sing 362 n n C5' C6' SOG sing 363 n n C5' "H5'1" SOG sing 364 n n C5' "H5'2" SOG sing 365 n n C6' C7' SOG sing 366 n n C6' "H6'1" SOG sing 367 n n C6' "H6'2" SOG sing 368 n n C7' C8' SOG sing 369 n n C7' "H7'1" SOG sing 370 n n C7' "H7'2" SOG sing 371 n n C8' "H8'1" SOG sing 372 n n C8' "H8'2" SOG sing 373 n n C8' "H8'3" SOG sing 374 n n O2 HO2 SOG sing 375 n n O3 HO3 SOG sing 376 n n O4 HO4 SOG sing 377 n n O6 HO6 SOG sing 378 n n # _atom_sites.entry_id 2YCZ _atom_sites.fract_transf_matrix[1][1] 0.005623 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00279 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017763 _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] 0.010063 _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 I32 A 1 400 400 I32 I32 . D 2 I32 B 1 400 400 I32 I32 . E 3 SOG B 1 1360 1360 SOG SOG . # 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 . . . E 3 47.807 -37.69 16.673 1 175.18 ? C1 SOG 1360 B 1 HETATM 2 C C2 SOG . . . E 3 47.407 -39.182 16.484 1 184.42 ? C2 SOG 1360 B 1 HETATM 3 C C3 SOG . . . E 3 47.447 -39.924 17.834 1 179.94 ? C3 SOG 1360 B 1 HETATM 4 C C4 SOG . . . E 3 48.808 -39.744 18.503 1 179.07 ? C4 SOG 1360 B 1 HETATM 5 C C5 SOG . . . E 3 49.085 -38.247 18.699 1 178.22 ? C5 SOG 1360 B 1 HETATM 6 C C6 SOG . . . E 3 50.492 -38.165 19.306 1 177.6 ? C6 SOG 1360 B 1 HETATM 7 C C1' SOG . . . E 3 48.544 -35.19 15.409 1 154.86 ? C1' SOG 1360 B 1 HETATM 8 C C2' SOG . . . E 3 48.648 -34.311 14.152 1 145.81 ? C2' SOG 1360 B 1 HETATM 9 C C3' SOG . . . E 3 47.301 -34.27 13.398 1 136.88 ? C3' SOG 1360 B 1 HETATM 10 C C4' SOG . . . E 3 47.393 -33.391 12.15 1 130.04 ? C4' SOG 1360 B 1 HETATM 11 C C5' SOG . . . E 3 46.022 -33.26 11.451 1 124.12 ? C5' SOG 1360 B 1 HETATM 12 C C6' SOG . . . E 3 46.122 -32.412 10.161 1 119.95 ? C6' SOG 1360 B 1 HETATM 13 C C7' SOG . . . E 3 46.619 -30.972 10.389 1 116.17 ? C7' SOG 1360 B 1 HETATM 14 C C8' SOG . . . E 3 46.729 -30.24 9.036 1 108.31 ? C8' SOG 1360 B 1 HETATM 15 S S1 SOG . . . E 3 47.996 -36.897 15.016 1 180.57 ? S1 SOG 1360 B 1 HETATM 16 O O2 SOG . . . E 3 46.088 -39.3 15.888 1 179.3 ? O2 SOG 1360 B 1 HETATM 17 O O3 SOG . . . E 3 47.206 -41.324 17.637 1 180.01 ? O3 SOG 1360 B 1 HETATM 18 O O4 SOG . . . E 3 48.816 -40.432 19.757 1 179.27 ? O4 SOG 1360 B 1 HETATM 19 O O5 SOG . . . E 3 49.045 -37.513 17.448 1 180.69 ? O5 SOG 1360 B 1 HETATM 20 O O6 SOG . . . E 3 51.385 -39.089 18.605 1 177.4 ? O6 SOG 1360 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #