data_5G53 # _model_server_result.job_id LgGcSGOV7uytp2Nf9Ga-dQ _model_server_result.datetime_utc '2024-11-28 00:53:25' _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 5g53 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":502}' # _entry.id 5G53 # _exptl.entry_id 5G53 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.434 _entity.id 4 _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 90 _cell.angle_gamma 90 _cell.entry_id 5G53 _cell.length_a 90.632 _cell.length_b 111.814 _cell.length_c 161.304 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5G53 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,E,F,G,I 1 1 B,D,H 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 ? 4 F N N ? 4 G 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 74 A CYS 74 1_555 A SG CYS 146 A CYS 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 77 A CYS 77 1_555 A SG CYS 166 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 259 A CYS 259 1_555 A SG CYS 262 A CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf5 B SG CYS 71 B CYS 71 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf6 B SG CYS 74 B CYS 74 1_555 B SG CYS 146 B CYS 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf7 B SG CYS 77 B CYS 77 1_555 B SG CYS 166 B CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 B SG CYS 259 B CYS 259 1_555 B SG CYS 262 B CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? # _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 373 n n C1 S1 SOG sing 374 n n C1 O5 SOG sing 375 n n C1 H1 SOG sing 376 n n C2 C3 SOG sing 377 n n C2 O2 SOG sing 378 n n C2 H2 SOG sing 379 n n C3 C4 SOG sing 380 n n C3 O3 SOG sing 381 n n C3 H3 SOG sing 382 n n C4 C5 SOG sing 383 n n C4 O4 SOG sing 384 n n C4 H4 SOG sing 385 n n C5 C6 SOG sing 386 n n C5 O5 SOG sing 387 n n C5 H5 SOG sing 388 n n C6 O6 SOG sing 389 n n C6 H61 SOG sing 390 n n C6 H62 SOG sing 391 n n C1' C2' SOG sing 392 n n C1' S1 SOG sing 393 n n C1' "H1'1" SOG sing 394 n n C1' "H1'2" SOG sing 395 n n C2' C3' SOG sing 396 n n C2' "H2'1" SOG sing 397 n n C2' "H2'2" SOG sing 398 n n C3' C4' SOG sing 399 n n C3' "H3'1" SOG sing 400 n n C3' "H3'2" SOG sing 401 n n C4' C5' SOG sing 402 n n C4' "H4'1" SOG sing 403 n n C4' "H4'2" SOG sing 404 n n C5' C6' SOG sing 405 n n C5' "H5'1" SOG sing 406 n n C5' "H5'2" SOG sing 407 n n C6' C7' SOG sing 408 n n C6' "H6'1" SOG sing 409 n n C6' "H6'2" SOG sing 410 n n C7' C8' SOG sing 411 n n C7' "H7'1" SOG sing 412 n n C7' "H7'2" SOG sing 413 n n C8' "H8'1" SOG sing 414 n n C8' "H8'2" SOG sing 415 n n C8' "H8'3" SOG sing 416 n n O2 HO2 SOG sing 417 n n O3 HO3 SOG sing 418 n n O4 HO4 SOG sing 419 n n O6 HO6 SOG sing 420 n n # _atom_sites.entry_id 5G53 _atom_sites.fract_transf_matrix[1][1] 0.011034 _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] 0.008943 _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] 0.006199 _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 E 3 NEC A 1 400 400 NEC NEC . F 4 SOG A 1 501 501 SOG SOG . G 4 SOG A 1 502 502 SOG SOG . H 3 NEC B 1 400 400 NEC NEC . I 5 GDP C 1 400 400 GDP GDP . # 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 . . . G 4 -19.749 -29.362 -1.313 1 144.03 ? C1 SOG 502 A 1 HETATM 2 C C2 SOG . . . G 4 -20.615 -28.887 -0.14 1 145.62 ? C2 SOG 502 A 1 HETATM 3 C C3 SOG . . . G 4 -20.061 -29.309 1.218 1 146.31 ? C3 SOG 502 A 1 HETATM 4 C C4 SOG . . . G 4 -19.626 -30.769 1.226 1 148.36 ? C4 SOG 502 A 1 HETATM 5 C C5 SOG . . . G 4 -18.712 -31.064 0.028 1 148.99 ? C5 SOG 502 A 1 HETATM 6 C C6 SOG . . . G 4 -18.228 -32.52 -0.031 1 146.36 ? C6 SOG 502 A 1 HETATM 7 C C1' SOG . . . G 4 -19.594 -29.793 -4.044 1 126.29 ? C1' SOG 502 A 1 HETATM 8 C C2' SOG . . . G 4 -20.238 -29.566 -5.411 1 124.47 ? C2' SOG 502 A 1 HETATM 9 C C3' SOG . . . G 4 -20.193 -28.098 -5.86 1 121.9 ? C3' SOG 502 A 1 HETATM 10 C C4' SOG . . . G 4 -21.504 -27.321 -5.667 1 114.25 ? C4' SOG 502 A 1 HETATM 11 C C5' SOG . . . G 4 -21.717 -26.249 -6.738 1 107.59 ? C5' SOG 502 A 1 HETATM 12 C C6' SOG . . . G 4 -20.799 -25.041 -6.56 1 102.58 ? C6' SOG 502 A 1 HETATM 13 C C7' SOG . . . G 4 -20.909 -24.097 -7.754 1 99.35 ? C7' SOG 502 A 1 HETATM 14 C C8' SOG . . . G 4 -20.097 -22.836 -7.545 1 97.19 ? C8' SOG 502 A 1 HETATM 15 S S1 SOG . . . G 4 -20.651 -29.111 -2.812 1 135.19 ? S1 SOG 502 A 1 HETATM 16 O O2 SOG . . . G 4 -20.706 -27.458 -0.161 1 146.74 ? O2 SOG 502 A 1 HETATM 17 O O3 SOG . . . G 4 -21.059 -29.1 2.225 1 143.31 ? O3 SOG 502 A 1 HETATM 18 O O4 SOG . . . G 4 -18.97 -31.02 2.474 1 148.76 ? O4 SOG 502 A 1 HETATM 19 O O5 SOG . . . G 4 -19.421 -30.749 -1.178 1 148.51 ? O5 SOG 502 A 1 HETATM 20 O O6 SOG . . . G 4 -16.807 -32.588 -0.233 1 140.16 ? O6 SOG 502 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #