data_2YCY # _model_server_result.job_id 9J35OVVWQlFUxIGcch5IBw _model_server_result.datetime_utc '2024-11-01 11:20:31' _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 2ycy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1361}' # _entry.id 2YCY # _exptl.entry_id 2YCY _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 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 111.27 _cell.angle_gamma 90 _cell.entry_id 2YCY _cell.length_a 184.76 _cell.length_b 56.161 _cell.length_c 89.778 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YCY _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,D,E,K 1 1 B,F,G,H,I,J,L 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 ? 3 D N N ? 3 E N N ? 3 G N N ? 3 H N N ? 3 I 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 84 A CYS 114 1_555 A SG CYS 169 A CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 A SG CYS 162 A CYS 192 1_555 A SG CYS 168 A CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? disulf ? disulf3 B SG CYS 84 B CYS 114 1_555 B SG CYS 169 B CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf4 B SG CYS 162 B CYS 192 1_555 B SG CYS 168 B CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc1 B O CYS 162 B CYS 192 1_555 J NA NA . B NA 1363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc2 B O ASP 165 B ASP 195 1_555 J NA NA . B NA 1363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc3 B O CYS 168 B CYS 198 1_555 J NA NA . B NA 1363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? # _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 333 n n C1 S1 SOG sing 334 n n C1 O5 SOG sing 335 n n C1 H1 SOG sing 336 n n C2 C3 SOG sing 337 n n C2 O2 SOG sing 338 n n C2 H2 SOG sing 339 n n C3 C4 SOG sing 340 n n C3 O3 SOG sing 341 n n C3 H3 SOG sing 342 n n C4 C5 SOG sing 343 n n C4 O4 SOG sing 344 n n C4 H4 SOG sing 345 n n C5 C6 SOG sing 346 n n C5 O5 SOG sing 347 n n C5 H5 SOG sing 348 n n C6 O6 SOG sing 349 n n C6 H61 SOG sing 350 n n C6 H62 SOG sing 351 n n C1' C2' SOG sing 352 n n C1' S1 SOG sing 353 n n C1' "H1'1" SOG sing 354 n n C1' "H1'2" SOG sing 355 n n C2' C3' SOG sing 356 n n C2' "H2'1" SOG sing 357 n n C2' "H2'2" SOG sing 358 n n C3' C4' SOG sing 359 n n C3' "H3'1" SOG sing 360 n n C3' "H3'2" SOG sing 361 n n C4' C5' SOG sing 362 n n C4' "H4'1" SOG sing 363 n n C4' "H4'2" SOG sing 364 n n C5' C6' SOG sing 365 n n C5' "H5'1" SOG sing 366 n n C5' "H5'2" SOG sing 367 n n C6' C7' SOG sing 368 n n C6' "H6'1" SOG sing 369 n n C6' "H6'2" SOG sing 370 n n C7' C8' SOG sing 371 n n C7' "H7'1" SOG sing 372 n n C7' "H7'2" SOG sing 373 n n C8' "H8'1" SOG sing 374 n n C8' "H8'2" SOG sing 375 n n C8' "H8'3" SOG sing 376 n n O2 HO2 SOG sing 377 n n O3 HO3 SOG sing 378 n n O4 HO4 SOG sing 379 n n O6 HO6 SOG sing 380 n n # _atom_sites.entry_id 2YCY _atom_sites.fract_transf_matrix[1][1] 0.005412 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002107 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017806 _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] 0.011953 _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 P32 A 1 400 400 P32 P32 . D 3 SOG A 1 1360 1360 SOG SOG . E 3 SOG A 1 1361 1361 SOG SOG . F 2 P32 B 1 400 400 P32 P32 . G 3 SOG B 1 1360 1360 SOG SOG . H 3 SOG B 1 1361 1361 SOG SOG . I 3 SOG B 1 1362 1362 SOG SOG . J 4 NA B 1 1363 1363 NA NA . K 5 HOH A 1 2001 2001 HOH HOH . L 5 HOH B 1 2001 2001 HOH HOH . L 5 HOH B 2 2002 2002 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 . . . E 3 34.785 24.785 -7.546 1 99.31 ? C1 SOG 1361 A 1 HETATM 2 C C2 SOG . . . E 3 35.903 24.149 -6.68 1 103.93 ? C2 SOG 1361 A 1 HETATM 3 C C3 SOG . . . E 3 36.395 25.162 -5.642 1 106.8 ? C3 SOG 1361 A 1 HETATM 4 C C4 SOG . . . E 3 36.865 26.423 -6.382 1 120.71 ? C4 SOG 1361 A 1 HETATM 5 C C5 SOG . . . E 3 35.717 27 -7.255 1 106.86 ? C5 SOG 1361 A 1 HETATM 6 C C6 SOG . . . E 3 36.2 28.286 -7.939 1 107.28 ? C6 SOG 1361 A 1 HETATM 7 C C1' SOG . . . E 3 35.5 23.608 -9.889 1 74.54 ? C1' SOG 1361 A 1 HETATM 8 C C2' SOG . . . E 3 35.446 22.539 -10.97 1 64.82 ? C2' SOG 1361 A 1 HETATM 9 C C3' SOG . . . E 3 34.206 22.636 -11.851 1 53.22 ? C3' SOG 1361 A 1 HETATM 10 C C4' SOG . . . E 3 32.974 21.985 -11.236 1 45.34 ? C4' SOG 1361 A 1 HETATM 11 C C5' SOG . . . E 3 33.156 20.463 -11.063 1 38.52 ? C5' SOG 1361 A 1 HETATM 12 C C6' SOG . . . E 3 31.843 19.75 -10.697 1 35.13 ? C6' SOG 1361 A 1 HETATM 13 C C7' SOG . . . E 3 32.044 18.234 -10.571 1 29.74 ? C7' SOG 1361 A 1 HETATM 14 C C8' SOG . . . E 3 30.773 17.433 -10.236 1 22.58 ? C8' SOG 1361 A 1 HETATM 15 S S1 SOG . . . E 3 34.146 23.482 -8.685 1 90.69 ? S1 SOG 1361 A 1 HETATM 16 O O2 SOG . . . E 3 35.423 22.955 -6.032 1 106.18 ? O2 SOG 1361 A 1 HETATM 17 O O3 SOG . . . E 3 37.433 24.585 -4.818 1 106.71 ? O3 SOG 1361 A 1 HETATM 18 O O4 SOG . . . E 3 37.305 27.384 -5.419 1 146.08 ? O4 SOG 1361 A 1 HETATM 19 O O5 SOG . . . E 3 35.33 25.989 -8.216 1 103.24 ? O5 SOG 1361 A 1 HETATM 20 O O6 SOG . . . E 3 37.209 27.966 -8.904 1 113.06 ? O6 SOG 1361 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #