data_4BVG # _model_server_result.job_id 8yc-glPU8ALcebVhuikeOA _model_server_result.datetime_utc '2026-10-25 02:00:57' _model_server_result.server_version 0.9.13 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4bvg # _entry.id 4BVG # _exptl.entry_id 4BVG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 31484.219 _entity.id 1 _entity.src_method man _entity.type polymer _entity.pdbx_description 'NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3,MITOCHONDRIAL' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment 'RESIDUES 116-399' _entity.pdbx_ec 3.5.1.- # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 4BVG _cell.length_a 78.023 _cell.length_b 131.329 _cell.length_c 76.508 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4BVG _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 1 _struct_asym.id A _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _entity_poly.entity_id 1 _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.type polypeptide(L) _entity_poly.pdbx_strand_id A _entity_poly.pdbx_seq_one_letter_code ;GSSDKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTL AKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMAD RVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHP RSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK ; _entity_poly.pdbx_seq_one_letter_code_can ;GSSDKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTL AKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMAD RVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHP RSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK ; _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.hetero _entity_poly_seq.mon_id _entity_poly_seq.num 1 n GLY 1 1 n SER 2 1 n SER 3 1 n ASP 4 1 n LYS 5 1 n GLY 6 1 n LYS 7 1 n LEU 8 1 n SER 9 1 n LEU 10 1 n GLN 11 1 n ASP 12 1 n VAL 13 1 n ALA 14 1 n GLU 15 1 n LEU 16 1 n ILE 17 1 n ARG 18 1 n ALA 19 1 n ARG 20 1 n ALA 21 1 n CYS 22 1 n GLN 23 1 n ARG 24 1 n VAL 25 1 n VAL 26 1 n VAL 27 1 n MET 28 1 n VAL 29 1 n GLY 30 1 n ALA 31 1 n GLY 32 1 n ILE 33 1 n SER 34 1 n THR 35 1 n PRO 36 1 n SER 37 1 n GLY 38 1 n ILE 39 1 n PRO 40 1 n ASP 41 1 n PHE 42 1 n ARG 43 1 n SER 44 1 n PRO 45 1 n GLY 46 1 n SER 47 1 n GLY 48 1 n LEU 49 1 n TYR 50 1 n SER 51 1 n ASN 52 1 n LEU 53 1 n GLN 54 1 n GLN 55 1 n TYR 56 1 n ASP 57 1 n LEU 58 1 n PRO 59 1 n TYR 60 1 n PRO 61 1 n GLU 62 1 n ALA 63 1 n ILE 64 1 n PHE 65 1 n GLU 66 1 n LEU 67 1 n PRO 68 1 n PHE 69 1 n PHE 70 1 n PHE 71 1 n HIS 72 1 n ASN 73 1 n PRO 74 1 n LYS 75 1 n PRO 76 1 n PHE 77 1 n PHE 78 1 n THR 79 1 n LEU 80 1 n ALA 81 1 n LYS 82 1 n GLU 83 1 n LEU 84 1 n TYR 85 1 n PRO 86 1 n GLY 87 1 n ASN 88 1 n TYR 89 1 n LYS 90 1 n PRO 91 1 n ASN 92 1 n VAL 93 1 n THR 94 1 n HIS 95 1 n TYR 96 1 n PHE 97 1 n LEU 98 1 n ARG 99 1 n LEU 100 1 n LEU 101 1 n HIS 102 1 n ASP 103 1 n LYS 104 1 n GLY 105 1 n LEU 106 1 n LEU 107 1 n LEU 108 1 n ARG 109 1 n LEU 110 1 n TYR 111 1 n THR 112 1 n GLN 113 1 n ASN 114 1 n ILE 115 1 n ASP 116 1 n GLY 117 1 n LEU 118 1 n GLU 119 1 n ARG 120 1 n VAL 121 1 n SER 122 1 n GLY 123 1 n ILE 124 1 n PRO 125 1 n ALA 126 1 n SER 127 1 n LYS 128 1 n LEU 129 1 n VAL 130 1 n GLU 131 1 n ALA 132 1 n HIS 133 1 n GLY 134 1 n THR 135 1 n PHE 136 1 n ALA 137 1 n SER 138 1 n ALA 139 1 n THR 140 1 n CYS 141 1 n THR 142 1 n VAL 143 1 n CYS 144 1 n GLN 145 1 n ARG 146 1 n PRO 147 1 n PHE 148 1 n PRO 149 1 n GLY 150 1 n GLU 151 1 n ASP 152 1 n ILE 153 1 n ARG 154 1 n ALA 155 1 n ASP 156 1 n VAL 157 1 n MET 158 1 n ALA 159 1 n ASP 160 1 n ARG 161 1 n VAL 162 1 n PRO 163 1 n ARG 164 1 n CYS 165 1 n PRO 166 1 n VAL 167 1 n CYS 168 1 n THR 169 1 n GLY 170 1 n VAL 171 1 n VAL 172 1 n LYS 173 1 n PRO 174 1 n ASP 175 1 n ILE 176 1 n VAL 177 1 n PHE 178 1 n PHE 179 1 n GLY 180 1 n GLU 181 1 n PRO 182 1 n LEU 183 1 n PRO 184 1 n GLN 185 1 n ARG 186 1 n PHE 187 1 n LEU 188 1 n LEU 189 1 n HIS 190 1 n VAL 191 1 n VAL 192 1 n ASP 193 1 n PHE 194 1 n PRO 195 1 n MET 196 1 n ALA 197 1 n ASP 198 1 n LEU 199 1 n LEU 200 1 n LEU 201 1 n ILE 202 1 n LEU 203 1 n GLY 204 1 n THR 205 1 n SER 206 1 n LEU 207 1 n GLU 208 1 n VAL 209 1 n GLU 210 1 n PRO 211 1 n PHE 212 1 n ALA 213 1 n SER 214 1 n LEU 215 1 n THR 216 1 n GLU 217 1 n ALA 218 1 n VAL 219 1 n ARG 220 1 n SER 221 1 n SER 222 1 n VAL 223 1 n PRO 224 1 n ARG 225 1 n LEU 226 1 n LEU 227 1 n ILE 228 1 n ASN 229 1 n ARG 230 1 n ASP 231 1 n LEU 232 1 n VAL 233 1 n GLY 234 1 n PRO 235 1 n LEU 236 1 n ALA 237 1 n TRP 238 1 n HIS 239 1 n PRO 240 1 n ARG 241 1 n SER 242 1 n ARG 243 1 n ASP 244 1 n VAL 245 1 n ALA 246 1 n GLN 247 1 n LEU 248 1 n GLY 249 1 n ASP 250 1 n VAL 251 1 n VAL 252 1 n HIS 253 1 n GLY 254 1 n VAL 255 1 n GLU 256 1 n SER 257 1 n LEU 258 1 n VAL 259 1 n GLU 260 1 n LEU 261 1 n LEU 262 1 n GLY 263 1 n TRP 264 1 n THR 265 1 n GLU 266 1 n GLU 267 1 n MET 268 1 n ARG 269 1 n ASP 270 1 n LEU 271 1 n VAL 272 1 n GLN 273 1 n ARG 274 1 n GLU 275 1 n THR 276 1 n GLY 277 1 n LYS 278 1 n LEU 279 1 n ASP 280 1 n GLY 281 1 n PRO 282 1 n ASP 283 1 n LYS 284 # 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 NZ LYS 5 B LYS 0 1_555 Q CH XYQ . B XYQ 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.367 ? metalc ? metalc1 A SG CYS 141 A CYS 256 1_555 P ZN ZN . A ZN 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc2 A SG CYS 144 A CYS 259 1_555 P ZN ZN . A ZN 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc3 A SG CYS 165 A CYS 280 1_555 P ZN ZN . A ZN 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc4 A SG CYS 168 A CYS 283 1_555 P ZN ZN . A ZN 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? # _chem_comp.formula 'C6 H15 N2 O2 1' _chem_comp.formula_weight 147.195 _chem_comp.id LYS _chem_comp.mon_nstd_flag y _chem_comp.name LYSINE _chem_comp.type 'l-peptide linking' _chem_comp.pdbx_synonyms ? # 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 N CA LYS sing 216 n n N H LYS sing 217 n n N H2 LYS sing 218 n n CA C LYS sing 219 n n CA CB LYS sing 220 n n CA HA LYS sing 221 n n C O LYS doub 222 n n C OXT LYS sing 223 n n CB CG LYS sing 224 n n CB HB2 LYS sing 225 n n CB HB3 LYS sing 226 n n CG CD LYS sing 227 n n CG HG2 LYS sing 228 n n CG HG3 LYS sing 229 n n CD CE LYS sing 230 n n CD HD2 LYS sing 231 n n CD HD3 LYS sing 232 n n CE NZ LYS sing 233 n n CE HE2 LYS sing 234 n n CE HE3 LYS sing 235 n n NZ HZ1 LYS sing 236 n n NZ HZ2 LYS sing 237 n n NZ HZ3 LYS sing 238 n n OXT HXT LYS sing 239 n n # _atom_sites.entry_id 4BVG _atom_sites.fract_transf_matrix[1][1] 0.012817 _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] 0.007614 _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] 0.013071 _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 3 EDO A 1 1396 1396 EDO EDO ? D 3 EDO A 1 1397 1397 EDO EDO ? E 3 EDO A 1 1398 1398 EDO EDO ? F 3 EDO A 1 1399 1399 EDO EDO ? G 4 GOL A 1 1400 1400 GOL GOL ? H 4 GOL A 1 1401 1401 GOL GOL ? I 4 GOL A 1 1402 1402 GOL GOL ? J 3 EDO A 1 1403 1403 EDO EDO ? K 3 EDO A 1 1404 1404 EDO EDO ? L 5 SO4 A 1 1405 1405 SO4 SO4 ? M 5 SO4 A 1 1406 1406 SO4 SO4 ? N 3 EDO A 1 1407 1407 EDO EDO ? O 6 PEG A 1 1408 1408 PEG PEG ? P 7 ZN A 1 1409 1409 ZN ZN ? Q 8 XYQ B 1 1000 1000 XYQ OAD ? R 9 HOH A 1 2001 2001 HOH HOH ? R 9 HOH A 2 2002 2002 HOH HOH ? R 9 HOH A 3 2003 2003 HOH HOH ? R 9 HOH A 4 2004 2004 HOH HOH ? R 9 HOH A 5 2005 2005 HOH HOH ? R 9 HOH A 6 2006 2006 HOH HOH ? R 9 HOH A 7 2007 2007 HOH HOH ? R 9 HOH A 8 2008 2008 HOH HOH ? R 9 HOH A 9 2009 2009 HOH HOH ? R 9 HOH A 10 2010 2010 HOH HOH ? R 9 HOH A 11 2011 2011 HOH HOH ? R 9 HOH A 12 2012 2012 HOH HOH ? R 9 HOH A 13 2013 2013 HOH HOH ? R 9 HOH A 14 2014 2014 HOH HOH ? R 9 HOH A 15 2015 2015 HOH HOH ? R 9 HOH A 16 2016 2016 HOH HOH ? R 9 HOH A 17 2017 2017 HOH HOH ? R 9 HOH A 18 2018 2018 HOH HOH ? R 9 HOH A 19 2019 2019 HOH HOH ? R 9 HOH A 20 2020 2020 HOH HOH ? R 9 HOH A 21 2021 2021 HOH HOH ? R 9 HOH A 22 2022 2022 HOH HOH ? R 9 HOH A 23 2023 2023 HOH HOH ? R 9 HOH A 24 2024 2024 HOH HOH ? R 9 HOH A 25 2025 2025 HOH HOH ? R 9 HOH A 26 2026 2026 HOH HOH ? R 9 HOH A 27 2027 2027 HOH HOH ? R 9 HOH A 28 2028 2028 HOH HOH ? R 9 HOH A 29 2029 2029 HOH HOH ? R 9 HOH A 30 2030 2030 HOH HOH ? R 9 HOH A 31 2031 2031 HOH HOH ? R 9 HOH A 32 2032 2032 HOH HOH ? R 9 HOH A 33 2033 2033 HOH HOH ? R 9 HOH A 34 2034 2034 HOH HOH ? R 9 HOH A 35 2035 2035 HOH HOH ? R 9 HOH A 36 2036 2036 HOH HOH ? R 9 HOH A 37 2037 2037 HOH HOH ? R 9 HOH A 38 2038 2038 HOH HOH ? R 9 HOH A 39 2039 2039 HOH HOH ? R 9 HOH A 40 2040 2040 HOH HOH ? R 9 HOH A 41 2041 2041 HOH HOH ? R 9 HOH A 42 2042 2042 HOH HOH ? R 9 HOH A 43 2043 2043 HOH HOH ? R 9 HOH A 44 2044 2044 HOH HOH ? R 9 HOH A 45 2045 2045 HOH HOH ? R 9 HOH A 46 2046 2046 HOH HOH ? R 9 HOH A 47 2047 2047 HOH HOH ? R 9 HOH A 48 2048 2048 HOH HOH ? R 9 HOH A 49 2049 2049 HOH HOH ? R 9 HOH A 50 2050 2050 HOH HOH ? R 9 HOH A 51 2051 2051 HOH HOH ? R 9 HOH A 52 2052 2052 HOH HOH ? R 9 HOH A 53 2053 2053 HOH HOH ? R 9 HOH A 54 2054 2054 HOH HOH ? R 9 HOH A 55 2055 2055 HOH HOH ? R 9 HOH A 56 2056 2056 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 ATOM 1 N N LYS 7 . . A 1 4.144 3.327 -19.787 1 63.39 ? N LYS 122 A 1 ATOM 2 C CA LYS 7 . . A 1 4.66 4.65 -19.324 1 62.3 ? CA LYS 122 A 1 ATOM 3 C C LYS 7 . . A 1 4.709 4.712 -17.773 1 60.58 ? C LYS 122 A 1 ATOM 4 O O LYS 7 . . A 1 3.663 4.591 -17.134 1 58.5 ? O LYS 122 A 1 ATOM 5 C CB LYS 7 . . A 1 3.797 5.768 -19.924 1 58.87 ? CB LYS 122 A 1 ATOM 6 C CG LYS 7 . . A 1 4.53 7.086 -20.108 1 64.28 ? CG LYS 122 A 1 ATOM 7 C CD LYS 7 . . A 1 4.481 7.586 -21.545 1 73.62 ? CD LYS 122 A 1 ATOM 8 C CE LYS 7 . . A 1 5.304 6.706 -22.485 1 72.28 ? CE LYS 122 A 1 ATOM 9 N NZ LYS 7 . . A 1 5.608 7.429 -23.752 1 72.3 ? NZ LYS 122 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 176 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 9 #