data_2VT4 # _model_server_result.job_id OpPttuV2PkKAO01f35yGlA _model_server_result.datetime_utc '2024-11-01 11:23:32' _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 2vt4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":405}' # _entry.id 2VT4 # _exptl.entry_id 2VT4 _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 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 67.6 _cell.angle_beta 73.3 _cell.angle_gamma 85.8 _cell.entry_id 2VT4 _cell.length_a 55.5 _cell.length_b 86.8 _cell.length_c 95.5 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VT4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 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 PQS dimeric 2 software_defined_assembly 1 PQS dimeric 2 software_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 ? monomeric 1 author_defined_assembly 5 ? monomeric 1 author_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J,K,L,M,N,O,AA,BA 1 1 C,D,P,Q,R,S,T,U,V,W,X,Y,Z,CA,DA 2 1 A,E,F,G,H,I,J,AA 3 1 B,K,L,M,N,O,BA 4 1 C,P,Q,R,S,T,U,CA 5 1 D,V,W,X,Y,Z,DA 6 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 G N N ? 4 H N N ? 4 I N N ? 4 M N N ? 4 N N N ? 4 O N N ? 4 R N N ? 4 S N N ? 4 T N N ? 4 X N N ? 4 Y N N ? 4 Z 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 A SG CYS 162 A CYS 192 1_555 A SG CYS 168 A CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf3 B SG CYS 84 B CYS 114 1_555 B SG CYS 169 B CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf4 B SG CYS 162 B CYS 192 1_555 B SG CYS 168 B CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf5 C SG CYS 84 C CYS 114 1_555 C SG CYS 169 C CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf6 C SG CYS 162 C CYS 192 1_555 C SG CYS 168 C CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf7 D SG CYS 84 D CYS 114 1_555 D SG CYS 169 D CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf8 D SG CYS 162 D CYS 192 1_555 D SG CYS 168 D CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc1 A O CYS 162 A CYS 192 1_555 F NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc2 A O ASP 165 A ASP 195 1_555 F NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc3 A O CYS 168 A CYS 198 1_555 F NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc4 F NA NA . A NA 401 1_555 AA O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc5 F NA NA . A NA 401 1_555 AA O HOH . A HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc6 B O ASP 165 B ASP 195 1_555 L NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc7 B O CYS 168 B CYS 198 1_555 L NA NA . B NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc8 C O ASP 165 C ASP 195 1_555 Q NA NA . C NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc9 C O CYS 168 C CYS 198 1_555 Q NA NA . C NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc10 Q NA NA . C NA 401 1_555 CA O HOH . C HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? metalc ? metalc11 D O CYS 162 D CYS 192 1_555 W NA NA . D NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc12 D O ASP 165 D ASP 195 1_555 W NA NA . D NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc13 D O CYS 168 D CYS 198 1_555 W NA NA . D NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc14 W NA NA . D NA 401 1_555 DA O HOH . D HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? # _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 364 n n C1 S1 SOG sing 365 n n C1 O5 SOG sing 366 n n C1 H1 SOG sing 367 n n C2 C3 SOG sing 368 n n C2 O2 SOG sing 369 n n C2 H2 SOG sing 370 n n C3 C4 SOG sing 371 n n C3 O3 SOG sing 372 n n C3 H3 SOG sing 373 n n C4 C5 SOG sing 374 n n C4 O4 SOG sing 375 n n C4 H4 SOG sing 376 n n C5 C6 SOG sing 377 n n C5 O5 SOG sing 378 n n C5 H5 SOG sing 379 n n C6 O6 SOG sing 380 n n C6 H61 SOG sing 381 n n C6 H62 SOG sing 382 n n C1' C2' SOG sing 383 n n C1' S1 SOG sing 384 n n C1' "H1'1" SOG sing 385 n n C1' "H1'2" SOG sing 386 n n C2' C3' SOG sing 387 n n C2' "H2'1" SOG sing 388 n n C2' "H2'2" SOG sing 389 n n C3' C4' SOG sing 390 n n C3' "H3'1" SOG sing 391 n n C3' "H3'2" SOG sing 392 n n C4' C5' SOG sing 393 n n C4' "H4'1" SOG sing 394 n n C4' "H4'2" SOG sing 395 n n C5' C6' SOG sing 396 n n C5' "H5'1" SOG sing 397 n n C5' "H5'2" SOG sing 398 n n C6' C7' SOG sing 399 n n C6' "H6'1" SOG sing 400 n n C6' "H6'2" SOG sing 401 n n C7' C8' SOG sing 402 n n C7' "H7'1" SOG sing 403 n n C7' "H7'2" SOG sing 404 n n C8' "H8'1" SOG sing 405 n n C8' "H8'2" SOG sing 406 n n C8' "H8'3" SOG sing 407 n n O2 HO2 SOG sing 408 n n O3 HO3 SOG sing 409 n n O4 HO4 SOG sing 410 n n O6 HO6 SOG sing 411 n n # _atom_sites.entry_id 2VT4 _atom_sites.fract_transf_matrix[1][1] 0.018018 _atom_sites.fract_transf_matrix[1][2] -0.001323 _atom_sites.fract_transf_matrix[1][3] -0.005298 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011552 _atom_sites.fract_transf_matrix[2][3] -0.0047 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.011803 _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 2 P32 A 1 400 400 P32 P32 . F 3 NA A 1 401 401 NA NA . G 4 SOG A 1 402 402 SOG SOG . H 4 SOG A 1 403 403 SOG SOG . I 4 SOG A 1 405 405 SOG SOG . J 5 D10 A 1 406 406 D10 D10 . K 2 P32 B 1 400 400 P32 P32 . L 3 NA B 1 401 401 NA NA . M 4 SOG B 1 402 402 SOG SOG . N 4 SOG B 1 404 404 SOG SOG . O 4 SOG B 1 405 405 SOG SOG . P 2 P32 C 1 400 400 P32 P32 . Q 3 NA C 1 401 401 NA NA . R 4 SOG C 1 402 402 SOG SOG . S 4 SOG C 1 404 404 SOG SOG . T 4 SOG C 1 405 405 SOG SOG . U 5 D10 C 1 406 406 D10 D10 . V 2 P32 D 1 400 400 P32 P32 . W 3 NA D 1 401 401 NA NA . X 4 SOG D 1 402 402 SOG SOG . Y 4 SOG D 1 403 403 SOG SOG . Z 4 SOG D 1 405 405 SOG SOG . AA 6 HOH A 1 2001 2001 HOH HOH . AA 6 HOH A 2 2002 2002 HOH HOH . AA 6 HOH A 3 2003 2003 HOH HOH . AA 6 HOH A 4 2004 2004 HOH HOH . AA 6 HOH A 5 2005 2005 HOH HOH . AA 6 HOH A 6 2006 2006 HOH HOH . AA 6 HOH A 7 2007 2007 HOH HOH . AA 6 HOH A 8 2008 2008 HOH HOH . AA 6 HOH A 9 2009 2009 HOH HOH . BA 6 HOH B 1 2001 2001 HOH HOH . BA 6 HOH B 2 2002 2002 HOH HOH . BA 6 HOH B 3 2003 2003 HOH HOH . BA 6 HOH B 4 2004 2004 HOH HOH . BA 6 HOH B 5 2005 2005 HOH HOH . BA 6 HOH B 6 2006 2006 HOH HOH . BA 6 HOH B 7 2007 2007 HOH HOH . CA 6 HOH C 1 2001 2001 HOH HOH . CA 6 HOH C 2 2002 2002 HOH HOH . CA 6 HOH C 3 2003 2003 HOH HOH . CA 6 HOH C 4 2004 2004 HOH HOH . CA 6 HOH C 5 2005 2005 HOH HOH . CA 6 HOH C 6 2006 2006 HOH HOH . CA 6 HOH C 7 2007 2007 HOH HOH . DA 6 HOH D 1 2001 2001 HOH HOH . DA 6 HOH D 2 2002 2002 HOH HOH . DA 6 HOH D 3 2003 2003 HOH HOH . DA 6 HOH D 4 2004 2004 HOH HOH . DA 6 HOH D 5 2005 2005 HOH HOH . DA 6 HOH D 6 2006 2006 HOH HOH . DA 6 HOH D 7 2007 2007 HOH HOH . DA 6 HOH D 8 2008 2008 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 . . . T 4 37.157 58.708 -25.164 1 128.17 ? C1 SOG 405 C 1 HETATM 2 C C2 SOG . . . T 4 35.962 59.366 -25.85 1 113.17 ? C2 SOG 405 C 1 HETATM 3 C C3 SOG . . . T 4 36.415 60.698 -26.415 1 112.55 ? C3 SOG 405 C 1 HETATM 4 C C4 SOG . . . T 4 36.884 61.555 -25.242 1 122.88 ? C4 SOG 405 C 1 HETATM 5 C C5 SOG . . . T 4 38.026 60.82 -24.548 1 119.94 ? C5 SOG 405 C 1 HETATM 6 C C6 SOG . . . T 4 38.582 61.596 -23.342 1 101.92 ? C6 SOG 405 C 1 HETATM 7 C C1' SOG . . . T 4 38.41 56.694 -24.018 1 107.27 ? C1' SOG 405 C 1 HETATM 8 C C2' SOG . . . T 4 38.593 55.247 -23.638 1 100.38 ? C2' SOG 405 C 1 HETATM 9 C C3' SOG . . . T 4 38.284 54.343 -24.824 1 86.85 ? C3' SOG 405 C 1 HETATM 10 C C4' SOG . . . T 4 38.42 52.957 -24.254 1 71.37 ? C4' SOG 405 C 1 HETATM 11 C C5' SOG . . . T 4 38.137 51.829 -25.213 1 60.36 ? C5' SOG 405 C 1 HETATM 12 C C6' SOG . . . T 4 38.244 50.604 -24.317 1 68.05 ? C6' SOG 405 C 1 HETATM 13 C C7' SOG . . . T 4 37.909 49.312 -25.03 1 65.16 ? C7' SOG 405 C 1 HETATM 14 C C8' SOG . . . T 4 37.986 48.177 -24.014 1 55.22 ? C8' SOG 405 C 1 HETATM 15 S S1 SOG . . . T 4 36.687 57.069 -24.511 1 124.14 ? S1 SOG 405 C 1 HETATM 16 O O2 SOG . . . T 4 35.519 58.547 -26.927 1 113.57 ? O2 SOG 405 C 1 HETATM 17 O O3 SOG . . . T 4 35.344 61.299 -27.142 1 111.69 ? O3 SOG 405 C 1 HETATM 18 O O4 SOG . . . T 4 37.378 62.807 -25.716 1 126.33 ? O4 SOG 405 C 1 HETATM 19 O O5 SOG . . . T 4 37.625 59.523 -24.061 1 114.48 ? O5 SOG 405 C 1 HETATM 20 O O6 SOG . . . T 4 39.704 60.891 -22.795 1 88.42 ? O6 SOG 405 C 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 20 #