data_2VNF # _model_server_result.job_id UVRNxR0ej14e3SEpjqKZgQ _model_server_result.datetime_utc '2025-03-22 22:45:16' _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 2vnf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1245}' # _entry.id 2VNF # _exptl.entry_id 2VNF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 154.251 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,3-DIHYDROXY-1,4-DITHIOBUTANE _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 90 _cell.angle_gamma 90 _cell.entry_id 2VNF _cell.length_a 68.516 _cell.length_b 68.516 _cell.length_c 28.174 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VNF _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43' # 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 author_and_software_defined_assembly 1 PQS 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,B,E,F,G,H,L,M 1 1 C,D,I,J,K,N,O 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 4 _struct_asym.id F _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 covale ? covale1 B C THR 3 B THR 3 1_555 B N M3L 4 B M3L 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 B C M3L 4 B M3L 4 1_555 B N GLN 5 B GLN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale3 D C THR 3 D THR 3 1_555 D N M3L 4 D M3L 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 D C M3L 4 D M3L 4 1_555 D N GLN 5 D GLN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 A SG CYS 13 A CYS 199 1_555 G ZN ZN . A ZN 1246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc2 A SG CYS 15 A CYS 201 1_555 G ZN ZN . A ZN 1246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc3 A SG CYS 26 A CYS 212 1_555 H ZN ZN . A ZN 1247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc4 A SG CYS 31 A CYS 217 1_555 H ZN ZN . A ZN 1247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc5 A ND1 HIS 37 A HIS 223 1_555 G ZN ZN . A ZN 1246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc6 A SG CYS 40 A CYS 226 1_555 G ZN ZN . A ZN 1246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc7 A SG CYS 53 A CYS 239 1_555 H ZN ZN . A ZN 1247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc8 A SG CYS 56 A CYS 242 1_555 H ZN ZN . A ZN 1247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc9 E NA NA . A NA 300 1_555 L O HOH . A HOH 2058 3_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc10 E NA NA . A NA 300 1_555 L O HOH . A HOH 2059 3_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc11 E NA NA . A NA 300 1_555 L O HOH . A HOH 2061 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc12 C SG CYS 13 C CYS 199 1_555 J ZN ZN . C ZN 1247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc13 C SG CYS 15 C CYS 201 1_555 J ZN ZN . C ZN 1247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc14 C SG CYS 26 C CYS 212 1_555 K ZN ZN . C ZN 1248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc15 C SG CYS 31 C CYS 217 1_555 K ZN ZN . C ZN 1248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc16 C ND1 HIS 37 C HIS 223 1_555 J ZN ZN . C ZN 1247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc17 C SG CYS 40 C CYS 226 1_555 J ZN ZN . C ZN 1247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc18 C SG CYS 53 C CYS 239 1_555 K ZN ZN . C ZN 1248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc19 C SG CYS 56 C CYS 242 1_555 K ZN ZN . C ZN 1248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? # _chem_comp.formula 'C4 H10 O2 S2' _chem_comp.formula_weight 154.251 _chem_comp.id DTT _chem_comp.mon_nstd_flag . _chem_comp.name 2,3-DIHYDROXY-1,4-DITHIOBUTANE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1,4-DITHIOTHREITOL # 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 S1 C1 DTT sing 83 n n S1 HS1 DTT sing 84 n n C1 C2 DTT sing 85 n n C1 H11 DTT sing 86 n n C1 H12 DTT sing 87 n n C2 O2 DTT sing 88 n n C2 C3 DTT sing 89 n n C2 H2 DTT sing 90 n n O2 HO2 DTT sing 91 n n C3 O3 DTT sing 92 n n C3 C4 DTT sing 93 n n C3 H3 DTT sing 94 n n O3 HO3 DTT sing 95 n n C4 S4 DTT sing 96 n n C4 H41 DTT sing 97 n n C4 H42 DTT sing 98 n n S4 HS2 DTT sing 99 n n # _atom_sites.entry_id 2VNF _atom_sites.fract_transf_matrix[1][1] 0.014595 _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] 0.014595 _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] 0.035494 _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 NA A 1 300 300 NA NA . F 4 DTT A 1 1245 1245 DTT DTT . G 5 ZN A 1 1246 1246 ZN ZN . H 5 ZN A 1 1247 1247 ZN ZN . I 6 DTU C 1 1246 1246 DTU DTU . J 5 ZN C 1 1247 1247 ZN ZN . K 5 ZN C 1 1248 1248 ZN ZN . L 7 HOH A 1 2001 2001 HOH HOH . L 7 HOH A 2 2002 2002 HOH HOH . L 7 HOH A 3 2003 2003 HOH HOH . L 7 HOH A 4 2004 2004 HOH HOH . L 7 HOH A 5 2005 2005 HOH HOH . L 7 HOH A 6 2006 2006 HOH HOH . L 7 HOH A 7 2007 2007 HOH HOH . L 7 HOH A 8 2008 2008 HOH HOH . L 7 HOH A 9 2009 2009 HOH HOH . L 7 HOH A 10 2010 2010 HOH HOH . L 7 HOH A 11 2011 2011 HOH HOH . L 7 HOH A 12 2012 2012 HOH HOH . L 7 HOH A 13 2013 2013 HOH HOH . L 7 HOH A 14 2014 2014 HOH HOH . L 7 HOH A 15 2015 2015 HOH HOH . L 7 HOH A 16 2016 2016 HOH HOH . L 7 HOH A 17 2017 2017 HOH HOH . L 7 HOH A 18 2018 2018 HOH HOH . L 7 HOH A 19 2019 2019 HOH HOH . L 7 HOH A 20 2020 2020 HOH HOH . L 7 HOH A 21 2021 2021 HOH HOH . L 7 HOH A 22 2022 2022 HOH HOH . L 7 HOH A 23 2023 2023 HOH HOH . L 7 HOH A 24 2024 2024 HOH HOH . L 7 HOH A 25 2025 2025 HOH HOH . L 7 HOH A 26 2026 2026 HOH HOH . L 7 HOH A 27 2027 2027 HOH HOH . L 7 HOH A 28 2028 2028 HOH HOH . L 7 HOH A 29 2029 2029 HOH HOH . L 7 HOH A 30 2030 2030 HOH HOH . L 7 HOH A 31 2031 2031 HOH HOH . L 7 HOH A 32 2032 2032 HOH HOH . L 7 HOH A 33 2033 2033 HOH HOH . L 7 HOH A 34 2034 2034 HOH HOH . L 7 HOH A 35 2035 2035 HOH HOH . L 7 HOH A 36 2036 2036 HOH HOH . L 7 HOH A 37 2037 2037 HOH HOH . L 7 HOH A 38 2038 2038 HOH HOH . L 7 HOH A 39 2039 2039 HOH HOH . L 7 HOH A 40 2040 2040 HOH HOH . L 7 HOH A 41 2041 2041 HOH HOH . L 7 HOH A 42 2042 2042 HOH HOH . L 7 HOH A 43 2043 2043 HOH HOH . L 7 HOH A 44 2044 2044 HOH HOH . L 7 HOH A 45 2045 2045 HOH HOH . L 7 HOH A 46 2046 2046 HOH HOH . L 7 HOH A 47 2047 2047 HOH HOH . L 7 HOH A 48 2048 2048 HOH HOH . L 7 HOH A 49 2049 2049 HOH HOH . L 7 HOH A 50 2050 2050 HOH HOH . L 7 HOH A 51 2051 2051 HOH HOH . L 7 HOH A 52 2052 2052 HOH HOH . L 7 HOH A 53 2053 2053 HOH HOH . L 7 HOH A 54 2054 2054 HOH HOH . L 7 HOH A 55 2056 2056 HOH HOH . L 7 HOH A 56 2057 2057 HOH HOH . L 7 HOH A 57 2058 2058 HOH HOH . L 7 HOH A 58 2059 2059 HOH HOH . L 7 HOH A 59 2060 2060 HOH HOH . L 7 HOH A 60 2061 2061 HOH HOH . M 7 HOH B 1 2001 2001 HOH HOH . M 7 HOH B 2 2002 2002 HOH HOH . M 7 HOH B 3 2003 2003 HOH HOH . M 7 HOH B 4 2004 2004 HOH HOH . M 7 HOH B 5 2005 2005 HOH HOH . M 7 HOH B 6 2006 2006 HOH HOH . M 7 HOH B 7 2007 2007 HOH HOH . M 7 HOH B 8 2008 2008 HOH HOH . N 7 HOH C 1 2001 2001 HOH HOH . N 7 HOH C 2 2002 2002 HOH HOH . N 7 HOH C 3 2003 2003 HOH HOH . N 7 HOH C 4 2004 2004 HOH HOH . N 7 HOH C 5 2005 2005 HOH HOH . N 7 HOH C 6 2006 2006 HOH HOH . N 7 HOH C 7 2007 2007 HOH HOH . N 7 HOH C 8 2008 2008 HOH HOH . N 7 HOH C 9 2009 2009 HOH HOH . N 7 HOH C 10 2010 2010 HOH HOH . N 7 HOH C 11 2011 2011 HOH HOH . N 7 HOH C 12 2012 2012 HOH HOH . N 7 HOH C 13 2013 2013 HOH HOH . N 7 HOH C 14 2014 2014 HOH HOH . N 7 HOH C 15 2015 2015 HOH HOH . N 7 HOH C 16 2016 2016 HOH HOH . N 7 HOH C 17 2017 2017 HOH HOH . N 7 HOH C 18 2018 2018 HOH HOH . N 7 HOH C 19 2019 2019 HOH HOH . N 7 HOH C 20 2020 2020 HOH HOH . N 7 HOH C 21 2021 2021 HOH HOH . N 7 HOH C 22 2022 2022 HOH HOH . N 7 HOH C 23 2023 2023 HOH HOH . N 7 HOH C 24 2024 2024 HOH HOH . N 7 HOH C 25 2025 2025 HOH HOH . N 7 HOH C 26 2026 2026 HOH HOH . N 7 HOH C 27 2027 2027 HOH HOH . N 7 HOH C 28 2028 2028 HOH HOH . N 7 HOH C 29 2029 2029 HOH HOH . N 7 HOH C 30 2030 2030 HOH HOH . N 7 HOH C 31 2031 2031 HOH HOH . N 7 HOH C 32 2032 2032 HOH HOH . N 7 HOH C 33 2034 2034 HOH HOH . N 7 HOH C 34 2035 2035 HOH HOH . N 7 HOH C 35 2036 2036 HOH HOH . N 7 HOH C 36 2037 2037 HOH HOH . N 7 HOH C 37 2038 2038 HOH HOH . N 7 HOH C 38 2039 2039 HOH HOH . N 7 HOH C 39 2040 2040 HOH HOH . N 7 HOH C 40 2041 2041 HOH HOH . O 7 HOH D 1 2001 2001 HOH HOH . O 7 HOH D 2 2002 2002 HOH HOH . O 7 HOH D 3 2003 2003 HOH HOH . O 7 HOH D 4 2004 2004 HOH HOH . O 7 HOH D 5 2005 2005 HOH HOH . O 7 HOH D 6 2006 2006 HOH HOH . O 7 HOH D 7 2007 2007 HOH HOH . O 7 HOH D 8 2008 2008 HOH HOH . O 7 HOH D 9 2009 2009 HOH HOH . O 7 HOH D 10 2010 2010 HOH HOH . O 7 HOH D 11 2011 2011 HOH HOH . O 7 HOH D 12 2012 2012 HOH HOH . O 7 HOH D 13 2013 2013 HOH HOH . O 7 HOH D 14 2014 2014 HOH HOH . O 7 HOH D 15 2015 2015 HOH HOH . O 7 HOH D 16 2016 2016 HOH HOH . O 7 HOH D 17 2017 2017 HOH HOH . O 7 HOH D 18 2018 2018 HOH HOH . O 7 HOH D 19 2019 2019 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 S S1 DTT . . . F 4 3.091 -12.298 -4.927 1 53.98 ? S1 DTT 1245 A 1 HETATM 2 C C1 DTT . . . F 4 4.288 -11.565 -6.02 1 26.84 ? C1 DTT 1245 A 1 HETATM 3 C C2 DTT . . . F 4 3.951 -10.13 -5.898 1 8.87 ? C2 DTT 1245 A 1 HETATM 4 O O2 DTT . . . F 4 4.366 -9.543 -7.122 1 37.26 ? O2 DTT 1245 A 1 HETATM 5 C C3 DTT . . . F 4 4.29 -9.217 -4.812 1 26.19 ? C3 DTT 1245 A 1 HETATM 6 O O3 DTT . . . F 4 4.115 -9.843 -3.565 1 39.51 ? O3 DTT 1245 A 1 HETATM 7 C C4 DTT . . . F 4 5.658 -8.688 -5.248 1 29.64 ? C4 DTT 1245 A 1 HETATM 8 S S4 DTT . . . F 4 5.512 -7.329 -6.43 1 62.37 ? S4 DTT 1245 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 8 #