NAD-dependent protein deacetylase sirtuin-2
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 52–356 | Fragment：residues52-356, lacking292-303 | myristoyl thiourea inhibitor, No.23 × 1 ZN ZINC ION × 1 F4R N-dodecylmethanethioamide × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.15M Potassium bromide, 30% (w/v) Polyethylene glycol monomethyl ether 2000 | Resolution 1.70 Å R-free 0.320 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 7BOT | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1J8F HUMAN SIRT2 HISTONE DEACETYLASE Deposited 2001-05-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
34–356（323 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；ethanol, bis-tris propane, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 277K
|
Resolution 1.70 Å R-free 0.260 |
| 1J8F HUMAN SIRT2 HISTONE DEACETYLASE Deposited 2001-05-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
34–356（323 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；ethanol, bis-tris propane, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 277K
|
Resolution 1.70 Å R-free 0.260 |
| 1J8F HUMAN SIRT2 HISTONE DEACETYLASE Deposited 2001-05-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
34–356（323 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；ethanol, bis-tris propane, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 277K
|
Resolution 1.70 Å R-free 0.260 |
| 3ZGO Re-refined structure of the human Sirt2 apoform Deposited 2012-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
34–356（323 aa）
|
Mutation：YES | ZN ZINC ION × 1 P6G HEXAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.63 Å R-free 0.195 |
| 3ZGO Re-refined structure of the human Sirt2 apoform Deposited 2012-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
34–356（323 aa）
|
Mutation：YES | ZN ZINC ION × 1 PGE TRIETHYLENE GLYCOL × 1 EOH ETHANOL × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.63 Å R-free 0.195 |
| 3ZGO Re-refined structure of the human Sirt2 apoform Deposited 2012-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
34–356（323 aa）
|
Mutation：YES | ZN ZINC ION × 1 PGE TRIETHYLENE GLYCOL × 5 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.63 Å R-free 0.195 |
| 3ZGV Structure of human SIRT2 in complex with ADP-ribose Deposited 2012-12-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
34–356（323 aa）
Fragment：RESIDUES 34-356
Chain B
34–356（323 aa）
Fragment：RESIDUES 34-356
|
Not recorded | ZN ZINC ION × 2 ACT ACETATE ION × 6 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 2 GOL GLYCEROL × 1 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；20% PEG 10 000, 100 MM AMMONIUM ACETATE, 100 MM BIS-TRIS PH 5.5
|
Resolution 2.27 Å R-free 0.188 |
| 4L3O Crystal Structure of SIRT2 in complex with the macrocyclic peptide S2iL5 Deposited 2013-06-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
55–356（302 aa）
Fragment：UNP residues 55-356
|
Not recorded | ZN ZINC ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；8.5% PEG 4000, 0.1M MES-NaOH, 0.1M Li2SO4, 0.1M NaCl, pH 7.0, vapor diffusion, sitting drop, temperature 277K
|
Resolution 2.52 Å R-free 0.263 |
| 4L3O Crystal Structure of SIRT2 in complex with the macrocyclic peptide S2iL5 Deposited 2013-06-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
55–356（302 aa）
Fragment：UNP residues 55-356
|
Not recorded | ZN ZINC ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；8.5% PEG 4000, 0.1M MES-NaOH, 0.1M Li2SO4, 0.1M NaCl, pH 7.0, vapor diffusion, sitting drop, temperature 277K
|
Resolution 2.52 Å R-free 0.263 |
| 4L3O Crystal Structure of SIRT2 in complex with the macrocyclic peptide S2iL5 Deposited 2013-06-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
55–356（302 aa）
Fragment：UNP residues 55-356
|
Not recorded | ZN ZINC ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；8.5% PEG 4000, 0.1M MES-NaOH, 0.1M Li2SO4, 0.1M NaCl, pH 7.0, vapor diffusion, sitting drop, temperature 277K
|
Resolution 2.52 Å R-free 0.263 |
| 4L3O Crystal Structure of SIRT2 in complex with the macrocyclic peptide S2iL5 Deposited 2013-06-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
55–356（302 aa）
Fragment：UNP residues 55-356
|
Not recorded | ZN ZINC ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；8.5% PEG 4000, 0.1M MES-NaOH, 0.1M Li2SO4, 0.1M NaCl, pH 7.0, vapor diffusion, sitting drop, temperature 277K
|
Resolution 2.52 Å R-free 0.263 |
| 4R8M Human SIRT2 crystal structure in complex with BHJH-TM1 Deposited 2014-09-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
38–356（319 aa）
Fragment：rossmann fold, UNP residues 38-356
|
Not recorded | ZN ZINC ION × 1 3LX tridecanethial × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25%(v/v) PEG3350, 0.1M Hepes buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.273 |
| 4R8M Human SIRT2 crystal structure in complex with BHJH-TM1 Deposited 2014-09-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
38–356（319 aa）
Fragment：rossmann fold, UNP residues 38-356
|
Not recorded | ZN ZINC ION × 1 3LX tridecanethial × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25%(v/v) PEG3350, 0.1M Hepes buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.273 |
| 4RMG Human Sirt2 in complex with SirReal2 and NAD+ Deposited 2014-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 3TE 2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]-N-[5-(naphthalen-1-ylmethyl)-1,3-thiazol-2-yl]acetamide × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1 M KSCN, 30% (wt/vol) PEG MME 2,000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.88 Å R-free 0.247 |
| 4RMG Human Sirt2 in complex with SirReal2 and NAD+ Deposited 2014-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 2 3TE 2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]-N-[5-(naphthalen-1-ylmethyl)-1,3-thiazol-2-yl]acetamide × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1 M KSCN, 30% (wt/vol) PEG MME 2,000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.88 Å R-free 0.247 |
| 4RMH Human Sirt2 in complex with SirReal2 and Ac-Lys-H3 peptide Deposited 2014-10-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP RESIDUES 56-356
|
Not recorded | ZN ZINC ION × 1 3TE 2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]-N-[5-(naphthalen-1-ylmethyl)-1,3-thiazol-2-yl]acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；2.8 M ammonium sulfate, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.42 Å R-free 0.188 |
| 4RMI Human Sirt2 in complex with SirReal1 and Ac-Lys-OTC peptide Deposited 2014-10-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 3TK N-(5-benzyl-1,3-thiazol-2-yl)-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；25% (wt/vol) PEG 3,350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.45 Å R-free 0.282 |
| 4RMJ Human Sirt2 in complex with ADP ribose and nicotinamide Deposited 2014-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
Chain B
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 2 NCA NICOTINAMIDE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1 ZN ZINC ION × 2 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.75；293 K；18% (wt/vol) PEG 10,000, pH 5.75, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.87 Å R-free 0.240 |
| 4X3O Sirt2 in complex with a myristoyl peptide Deposited 2014-12-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
52–355（304 aa）
Fragment：UNP RESIDUES 52-355
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 3Y0 [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R)-3-oxidanyl-5-sulfanyl-4-tridecoxy-oxolan-2-yl]methyl hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；300 K；25% PEG 3350, 0.1M HEPES, 5% Glycerol
|
Resolution 1.50 Å R-free 0.157 |
| 4X3P Sirt2 in complex with a myristoyl peptide Deposited 2014-12-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
52–355（304 aa）
Fragment：UNP RESIDUES 52-355
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 3LX tridecanethial × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；300 K；25% PEG 3350, 0.1M HEPES, 5% Glycerol
|
Resolution 1.80 Å R-free 0.173 |
| 4Y6L Human SIRT2 in complex with myristoylated peptide (H3K9myr) Deposited 2015-02-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
52–356（305 aa）
Fragment：UNP RESIDUES 52-356
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350
|
Resolution 1.60 Å R-free 0.232 |
| 4Y6L Human SIRT2 in complex with myristoylated peptide (H3K9myr) Deposited 2015-02-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
52–356（305 aa）
Fragment：UNP RESIDUES 52-356
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350
|
Resolution 1.60 Å R-free 0.232 |
| 4Y6O Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr) Deposited 2015-02-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
52–356（305 aa）
Fragment：UNP RESIDUES 52-291, 304-356
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350
|
Resolution 1.60 Å R-free 0.235 |
| 4Y6O Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr) Deposited 2015-02-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
52–356（305 aa）
Fragment：UNP RESIDUES 52-291, 304-356
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350
|
Resolution 1.60 Å R-free 0.235 |
| 4Y6Q Human SIRT2 in complex with 2-O-myristoyl-ADP-ribose Deposited 2015-02-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
52–356（305 aa）
Fragment：UNP RESIDUES 52-291, 304-356
Chain B
52–356（305 aa）
Fragment：UNP RESIDUES 52-291, 304-356
Chain C
52–356（305 aa）
Fragment：UNP RESIDUES 52-291, 304-356
Chain D
52–356（305 aa）
Fragment：UNP RESIDUES 52-291, 304-356
|
Not recorded | ZN ZINC ION × 4 OMR [(2S,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] tetradecanoate × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 2000
|
Resolution 1.90 Å R-free 0.267 |
| 5D7O Crystal structure of Sirt2-ADPR at an improved resolution Deposited 2015-08-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
50–356（307 aa）
Fragment：UNP residues 30-336
Chain B
50–356（307 aa）
Fragment：UNP residues 30-336
|
Not recorded | ZN ZINC ION × 2 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 2 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.25；277 K；0.2 M sodium chloride, 30 % (w/v) PEG 3350, 0.1 M Bis-Tris
|
Resolution 1.63 Å R-free 0.191 |
| 5D7P Crystal structure of human Sirt2 in complex with ADPR and EX-243 Deposited 2015-08-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
Chain B
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 2 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 2 OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 4 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.75；293 K；18 % (w/v) PEG 10000, 0.1 M Bis-Tris
|
Resolution 1.76 Å R-free 0.224 |
| 5D7Q Crystal structure of human Sirt2 in complex with ADPR and CHIC35 Deposited 2015-08-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
36–336（301 aa）
Fragment：UNP residues 56-356
Chain B
36–336（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 2 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 2 4I5 (6S)-2-chloro-5,6,7,8,9,10-hexahydrocyclohepta[b]indole-6-carboxamide × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.75；293 K；18 % (w/v) PEG 10000, 0.1 M Bis-Tris
|
Resolution 2.01 Å R-free 0.225 |
| 5DY4 Crystal structure of human Sirt2 in complex with a brominated 2nd generation SirReal inhibitor and NAD+ Deposited 2015-09-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：residues 56-356
|
Not recorded | ZN ZINC ION × 2 5GN N-{5-[(7-bromonaphthalen-1-yl)methyl]-1,3-thiazol-2-yl}-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；278 K；27 % PEG 3350
|
Resolution 1.77 Å R-free 0.213 |
| 5DY4 Crystal structure of human Sirt2 in complex with a brominated 2nd generation SirReal inhibitor and NAD+ Deposited 2015-09-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：residues 56-356
|
Not recorded | ZN ZINC ION × 1 5GN N-{5-[(7-bromonaphthalen-1-yl)methyl]-1,3-thiazol-2-yl}-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；278 K；27 % PEG 3350
|
Resolution 1.77 Å R-free 0.213 |
| 5DY5 Crystal structure of human Sirt2 in complex with a SirReal probe fragment Deposited 2015-09-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 2 5GR N-(5-{3-[(1-benzyl-1H-1,2,3-triazol-4-yl)methoxy]benzyl}-1,3-thiazol-2-yl)-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide × 2 EDO 1,2-ETHANEDIOL × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 BU3 (R,R)-2,3-BUTANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；17.5 % (wt/v) PEG 3350, 0.1 M HEPES
|
Resolution 1.95 Å R-free 0.205 |
| 5DY5 Crystal structure of human Sirt2 in complex with a SirReal probe fragment Deposited 2015-09-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 5GR N-(5-{3-[(1-benzyl-1H-1,2,3-triazol-4-yl)methoxy]benzyl}-1,3-thiazol-2-yl)-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide × 1 EDO 1,2-ETHANEDIOL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 BU3 (R,R)-2,3-BUTANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；277 K；17.5 % (wt/v) PEG 3350, 0.1 M HEPES
|
Resolution 1.95 Å R-free 0.205 |
| 5FYQ Sirt2 in complex with a 13-mer trifluoroacetylated Ran peptide Deposited 2016-03-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–356（356 aa）
Fragment：50-356
|
Not recorded | SO4 SULFATE ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；0.1 M HEPES PH 7.5 2.0M NH4SO4
|
Resolution 3.00 Å R-free 0.271 |
| 5FYQ Sirt2 in complex with a 13-mer trifluoroacetylated Ran peptide Deposited 2016-03-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–356（356 aa）
Fragment：50-356
|
Not recorded | SO4 SULFATE ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；0.1 M HEPES PH 7.5 2.0M NH4SO4
|
Resolution 3.00 Å R-free 0.271 |
| 5G4C Human SIRT2 catalyse short chain fatty acyl lysine Deposited 2016-05-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
34–356（323 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 34-356
|
Not recorded | ZN ZINC ION × 1 CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；12% PEG 8K, 0.1 M HEPES, PH 7.5, 5% ISOPROPANOL
|
Resolution 2.10 Å R-free 0.220 |
| 5G4C Human SIRT2 catalyse short chain fatty acyl lysine Deposited 2016-05-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
34–356（323 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 34-356
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；12% PEG 8K, 0.1 M HEPES, PH 7.5, 5% ISOPROPANOL
|
Resolution 2.10 Å R-free 0.220 |
| 5MAR Structure of human SIRT2 in complex with 1,2,4-Oxadiazole inhibitor and ADP ribose. Deposited 2016-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
|
Not recorded | ZN ZINC ION × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 7KE 3-[3-(4-chlorophenyl)-1,2,4-oxadiazol-5-yl]propan-1-ol × 1 EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 5 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；15-18 % PEG 10,000, 0.1M ammonium acetate, and 0.1M Bis-Tris pH 5.8
|
Resolution 1.89 Å R-free 0.194 |
| 5MAR Structure of human SIRT2 in complex with 1,2,4-Oxadiazole inhibitor and ADP ribose. Deposited 2016-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
56–356（301 aa）
|
Not recorded | ZN ZINC ION × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 7KE 3-[3-(4-chlorophenyl)-1,2,4-oxadiazol-5-yl]propan-1-ol × 1 DMS DIMETHYL SULFOXIDE × 4 GOL GLYCEROL × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；15-18 % PEG 10,000, 0.1M ammonium acetate, and 0.1M Bis-Tris pH 5.8
|
Resolution 1.89 Å R-free 0.194 |
| 5MAT Structure of human Sirtuin 2 in complex with a selective thienopyrimidinone based inhibitor Deposited 2016-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Chain C
56–356（301 aa）
|
Not recorded | ZN ZINC ION × 2 7KJ (7~{R})-7-[(3,5-dimethyl-1,2-oxazol-4-yl)methylamino]-3-[(4-methoxynaphthalen-1-yl)methyl]-5,6,7,8-tetrahydro-[1]benzothiolo[2,3-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 14 PG4 TETRAETHYLENE GLYCOL × 1 P6G HEXAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.83；293 K；2.6M ammonium sulfate, 5% PEG 300, 0.1 M MES
|
Resolution 2.07 Å |
| 5Y0Z Human SIRT2 in complex with a specific inhibitor, NPD11033 Deposited 2017-07-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
52–356（305 aa）
Fragment：UNP residues 52-356
|
Mutation：deletion mutation 292-303 | ZN ZINC ION × 1 8K9 (1~{R},9~{S})-11-[(2~{R})-3-[2,4-bis(2-methylbutan-2-yl)phenoxy]-2-oxidanyl-propyl]-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25%(w/v) PEG 3350, 0.1M BisTris, pH 5.5
|
Resolution 2.00 Å R-free 0.242 |
| 5Y0Z Human SIRT2 in complex with a specific inhibitor, NPD11033 Deposited 2017-07-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
52–356（305 aa）
Fragment：UNP residues 52-356
|
Mutation：deletion mutation 292-303 | ZN ZINC ION × 1 8K9 (1~{R},9~{S})-11-[(2~{R})-3-[2,4-bis(2-methylbutan-2-yl)phenoxy]-2-oxidanyl-propyl]-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25%(w/v) PEG 3350, 0.1M BisTris, pH 5.5
|
Resolution 2.00 Å R-free 0.242 |
| 5Y5N Crystal structure of human Sirtuin 2 in complex with a selective inhibitor Deposited 2017-08-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
34–356（323 aa）
|
Not recorded | ZN ZINC ION × 1 8NO 2-[[3-(2-phenylethoxy)phenyl]amino]benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；289 K；0.1M Bis-Tris buffer pH 5.5
15%(w/v) PEG5000 MME
|
Resolution 2.30 Å R-free 0.252 |
| 5YQL Crystal structure of Sirt2 in complex with selective inhibitor A2I Deposited 2017-11-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
|
Not recorded | A2I 2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-N-[3-(phenoxymethyl)phenyl]ethanamide × 1 ZN ZINC ION × 1 BME BETA-MERCAPTOETHANOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Magnesium Formate, 23-30% (v/v) Polyethylene glycol 3350
|
Resolution 1.60 Å R-free 0.185 |
| 5YQM Crystal structure of Sirt2 in complex with selective inhibitor A29 Deposited 2017-11-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
|
Not recorded | ZN ZINC ION × 1 A2X 2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-N-(4-phenylsulfanylphenyl)ethanamide × 1 BME BETA-MERCAPTOETHANOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES PH6.8, 25%-30% PEG 3350
|
Resolution 1.74 Å R-free 0.220 |
| 5YQN Crystal structure of Sirt2 in complex with selective inhibitor L55 Deposited 2017-11-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
|
Not recorded | ZN ZINC ION × 1 L55 N-[3-[[3-[2-(4,6-dimethylpyrimidin-2-yl)sulfanylethanoylamino]phenyl]methoxy]phenyl]-1-methyl-pyrazole-4-carboxamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES PH7.4, 30% PEG 3350
|
Resolution 1.60 Å R-free 0.204 |
| 5YQO Crystal structure of Sirt2 in complex with selective inhibitor L5C Deposited 2017-11-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
|
Not recorded | ZN ZINC ION × 1 L5C N-[4-[[3-[2-(4,6-dimethylpyrimidin-2-yl)sulfanylethanoylamino]phenyl]methoxy]phenyl]-1-methyl-pyrazole-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；2.1M DL-malic acid PH7.0
|
Resolution 1.48 Å R-free 0.193 |
| 6L65 Sirtuin 2 protein with H3K18 myristoylated peptide Deposited 2019-10-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
50–355（306 aa）
|
Not recorded | ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.5；293.1 K；0.1M MES, pH 6.5, 6%-20% (w/v) PEG 10000
|
Resolution 1.80 Å R-free 0.218 |
| 6L66 Sirtuin 2 protein with H3K18 myristoylated peptide and intact NAD molecule Deposited 2019-10-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
52–355（304 aa）
|
Not recorded | ZN ZINC ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 3LX tridecanethial × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6.5；291.15 K；0.1M MES, pH 6.5, 6%-20% (w/v) PEG 10000
|
Resolution 2.17 Å R-free 0.234 |
| 6L71 Sirtuin 2 demyristoylation native intermediate I & II mixture Deposited 2019-10-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
52–355（304 aa）
|
Not recorded | NCA NICOTINAMIDE × 1 YOY [[(2S,3aS,5S,6R,6aS)-2-dodecyl-6-oxidanyl-3a,5,6,6a-tetrahydrofuro[2,3-d][1,3]dioxol-5-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 YDD [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1M MES, pH 6.5, 6%-20% (w/v) PEG 10000
|
Resolution 2.11 Å R-free 0.224 |
| 6L72 Sirtuin 2 demyristoylation native final product Deposited 2019-10-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
52–355（304 aa）
|
Not recorded | OMR [(2S,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] tetradecanoate × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1M MES, pH=6.5, 6%-20% (w/v) PEG10000
|
Resolution 2.50 Å R-free 0.243 |
| 6NR0 SIRT2(56-356) with covalent intermediate between mechanism-based inhibitor Glucose-TM-1beta and 1'-SH ADP-ribose Deposited 2019-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: monomeric |
Chain A
1–319（319 aa）
Chain B
1–319（319 aa）
|
Not recorded | ZN ZINC ION × 2 KXJ N~2~-[3-(2-hydroxyethoxy)propanoyl]-N-phenyl-N~6~-tetradecanethioyl-L-lysinamide × 2 KXG [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-sulfanyl-oxolan-2-yl]methyl hydrogen phosphate × 2 NA SODIUM ION × 4 SO4 SULFATE ION × 2 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；Mixed solution of 0.44 mM protein (in buffer of 20 mM Tris/HCl pH 7.5, 160 mM NaCl) 2.5 mM NAD+, 2.5 mM Glucose-TM-1beta with an equal volume of well solution of 2 M (NH4)2SO4, 80 mM Na Acetate/HCl pH 5.0
|
Resolution 2.45 Å R-free 0.256 |
| 6NR0 SIRT2(56-356) with covalent intermediate between mechanism-based inhibitor Glucose-TM-1beta and 1'-SH ADP-ribose Deposited 2019-01-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–319（319 aa）
|
Not recorded | ZN ZINC ION × 1 KXJ N~2~-[3-(2-hydroxyethoxy)propanoyl]-N-phenyl-N~6~-tetradecanethioyl-L-lysinamide × 1 KXG [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-sulfanyl-oxolan-2-yl]methyl hydrogen phosphate × 1 NA SODIUM ION × 2 SO4 SULFATE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；Mixed solution of 0.44 mM protein (in buffer of 20 mM Tris/HCl pH 7.5, 160 mM NaCl) 2.5 mM NAD+, 2.5 mM Glucose-TM-1beta with an equal volume of well solution of 2 M (NH4)2SO4, 80 mM Na Acetate/HCl pH 5.0
|
Resolution 2.45 Å R-free 0.256 |
| 6QCN Human Sirt2 in complex with ADP-ribose and the inhibitor quercetin Deposited 2018-12-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
55–356（302 aa）
|
Not recorded | ZN ZINC ION × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 QUE 3,5,7,3',4'-PENTAHYDROXYFLAVONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；14% PEG 10,000, 0.1M ammonium acetate pH 5.8
|
Resolution 2.23 Å R-free 0.234 |
| 6QCN Human Sirt2 in complex with ADP-ribose and the inhibitor quercetin Deposited 2018-12-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
55–356（302 aa）
|
Not recorded | ZN ZINC ION × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；14% PEG 10,000, 0.1M ammonium acetate pH 5.8
|
Resolution 2.23 Å R-free 0.234 |
| 7BOS Human SIRT2 in complex with myristoyl thiourea inhibitor, No.13 Deposited 2020-03-19 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
52–356（305 aa）
Fragment：residues52-356, lacking292-303
|
Not recorded | ZN ZINC ION × 1 F4R N-dodecylmethanethioamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M HEPES pH 7.0, 30% v/v Jeffamine ED-2001
|
Resolution 1.70 Å R-free 0.263 |
| 7T1D Human SIRT2 in complex with small molecule 359 Deposited 2021-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Chain B
56–356（301 aa）
|
Not recorded | ZN ZINC ION × 2 SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 7 DMS DIMETHYL SULFOXIDE × 2 E7K 7-(2,4-dimethyl-1H-imidazol-1-yl)-2-(5-{[4-(1H-pyrazol-1-yl)phenyl]methyl}-1,3-thiazol-2-yl)-1,2,3,4-tetrahydroisoquinoline × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；Crystals of SIRT2 in complex with FLS-359 were obtained using hanging-drop vapour diffusion setups. SIRT2 at a concentration of 21.9 mg/ml (50 mM Hepes-NaOH, 150 mM NaCl, pH 8.0) was preincubated with 3.6 mM (5.7-fold molar excess) of FLS-359 (100 mM in DMSO) for 1 h.
1 ul of the protein solution was then mixed with 2 ul of reservoir solution (0.1 M Hepes-NaOH pH
6.6, 0.3 M Li2SO4, 21 % (w/v) PEG 3350) and streak seeded before being equilibrated at 20C over
0.2 ml of reservoir solution. Well diffracting crystals grew as thick aggregates of thin plates and were mounted within 19 days
|
Resolution 1.75 Å R-free 0.213 |
| 8OWZ Crystal structure of human Sirt2 in complex with a triazole-based SirReal Deposited 2023-04-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | KZU 2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-N-[5-[[3-[[1-(2-methoxyethyl)-1,2,3-triazol-4-yl]methoxy]phenyl]methyl]-1,3-thiazol-2-yl]ethanamide × 1 EDO 1,2-ETHANEDIOL × 4 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 BU3 (R,R)-2,3-BUTANEDIOL × 2 ZN ZINC ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；25 % PEG 3,350 , 0.1 M Bis-Tris pH 6.5
|
Resolution 1.65 Å R-free 0.198 |
| 8PY3 Crystal structure of human Sirt2 in complex with a 1,2,4-oxadiazole based inhibitor Deposited 2023-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 I1R 4-chloranyl-~{N}-[4-[5-[[(3~{S})-1-[(3-fluoranyl-2-methyl-phenyl)methyl]piperidin-3-yl]methyl]-1,2,4-oxadiazol-3-yl]phenyl]benzamide × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；25 % PEG 3,350, 0.22 M Bis-Tris pH 6.5
|
Resolution 1.65 Å R-free 0.185 |
| 8QOO Crystal structure of human Sirt2 in complex with the peptide-based pseudo-inhibitor TNFn-4.1 Deposited 2023-09-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 BU3 (R,R)-2,3-BUTANEDIOL × 1 EDO 1,2-ETHANEDIOL × 1 WH8 (2S,3S)-3-dodecylsulfanyl-2-methyl-butanoic acid × 1 WGN (2S,3R)-3-dodecylsulfanyl-2-methyl-butanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；19 % (w/v) PEG 3,350 in 0.1 M Bis-Tris pH 6.25
|
Resolution 1.55 Å R-free 0.190 |
| 8QT0 Crystal structure of human Sirt2 in complex with the super-slow substrate TNFn-3 Deposited 2023-10-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 3 WWE 3-dodecylsulfanyl-3-methyl-butanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；6.25 % (w/v) PEG 2,000, 6.25 % (w/v) PEG 3,350, 6.25 % (w/v) PEG 4,000, 6.25 % (w/v) PEG MME 5,000, 0.1 M HEPES pH 7.5
|
Resolution 1.85 Å R-free 0.213 |
| 8QT1 Crystal structure of human Sirt2 in complex with the super-slow substrate TNFn-5 Deposited 2023-10-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 WU3 (2S)-2-dodecylsulfanylpropanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；25 % (w/v) PEG 3,350 in 0.1 M Tris pH 8.5
|
Resolution 1.55 Å R-free 0.194 |
| 8QT2 Crystal structure of human Sirt2 in complex with the super-slow substrate TNFn-6 Deposited 2023-10-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 BU3 (R,R)-2,3-BUTANEDIOL × 1 WU8 3-dodecylsulfanyl-2,2-dimethyl-propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；26.5 % (w/v) PEG 3,350 in 0.1 M Bis-Tris pH 6.5.
|
Resolution 1.65 Å R-free 0.197 |
| 8QT3 Crystal structure of human Sirt2 in complex with the super-slow substrate TNFn-5 and NAD+ Deposited 2023-10-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 WU3 (2S)-2-dodecylsulfanylpropanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；24 % (w/v) PEG 3,350 in 0.1 M Bis-Tris pH 6.0
|
Resolution 1.55 Å R-free 0.201 |
| 8QT4 Crystal structure of human Sirt2 in complex with the super-slow substrate TNFn-6 and NAD+ Deposited 2023-10-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 4 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 DMS DIMETHYL SULFOXIDE × 1 BU3 (R,R)-2,3-BUTANEDIOL × 1 PGE TRIETHYLENE GLYCOL × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 WU8 3-dodecylsulfanyl-2,2-dimethyl-propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；25 % (w/v) PEG 3,350 in 0.1 M Bis-Tris pH 6.5
|
Resolution 1.55 Å R-free 0.188 |
| 8QT8 Crystal structure of human Sirt2 in complex with a TNFa-Myr analogue TNFn-34 Deposited 2023-10-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 WWK 3-dodecylsulfanylpropanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；19 % (w/v) PEG 3,350 in 0.1 M Bis-Tris pH 6.7
|
Resolution 1.65 Å R-free 0.212 |
| 8QTU Crystal structure of human Sirt2 in complex with the super-slow substrate TNFn-3 and NAD+ Deposited 2023-10-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 EDO 1,2-ETHANEDIOL × 1 WWE 3-dodecylsulfanyl-3-methyl-butanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；21.5 % (w/v) PEG 3,350 in 0.1 M Bis-Tris pH 6.25
|
Resolution 1.80 Å R-free 0.207 |
| 8TGP Crystal structure of SIRT2 with FAM-PEG4-H4K16(myristoyl) peptide Deposited 2023-07-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
34–356（323 aa）
|
Not recorded | ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M MES monohydrate pH 6.5 (NaOH), 20% w/v PEG 4,000
|
Resolution 1.76 Å R-free 0.230 |
| 8XE7 Crystal structure of human Sirt2 without Sirt2-specific insertion Deposited 2023-12-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
52–357（306 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；288 K；Bis-Tris (pH6.0), PEG 3350
|
Resolution 1.95 Å R-free 0.256 |
| 9DPD Cryo-EM structure of SerRS dimer in complex with one SIRT2 Deposited 2024-09-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–389（389 aa）
|
Not recorded | AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.87 Å |
| 9DPI Cryo-EM structure of SerRS dimer in complex with two SIRT2 Deposited 2024-09-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
1–389（389 aa）
Chain E
1–389（389 aa）
|
Not recorded | AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；in 25mM HEPES-Na pH7.5, 150mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 9FDR Crystal structure of human Sirt2 in apo form with opened selectivity pocket Deposited 2024-05-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 DMS DIMETHYL SULFOXIDE × 3 PG4 TETRAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；31 % (w/v) PEG 3,350, 0.1 M HEPES pH 7.5
|
Resolution 1.25 Å R-free 0.189 |
| 9FDS Crystal structure of human Sirt2 in complex with SirReal2 Deposited 2024-05-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 1 DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 3 3TE 2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]-N-[5-(naphthalen-1-ylmethyl)-1,3-thiazol-2-yl]acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；27 % (w/v) PEG 3,350, 0.1 M HEPES pH 7.75; Inhibitor has been soaked in same condition with addition of 10 % (v/v) DMSO for 24h.
|
Resolution 1.40 Å R-free 0.198 |
| 9FDT Crystal structure of human Sirt2 in complex with a pyrazole-based fragment inhibitor Deposited 2024-05-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 3 A1IBW [2-[2-methyl-5-(trifluoromethyl)pyrazol-3-yl]phenyl]methanol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；33 % (w/v) PEG 3,350, 0.1 M HEPES pH 7.75; Inhibitor has been soaked in same condition with addition of 10 % (v/v) DMSO for 24h.
|
Resolution 1.60 Å R-free 0.210 |
| 9FDU Crystal structure of human Sirt2 in complex with a pyridine-3-carbothioamide-based fragment inhibitor Deposited 2024-05-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 3 A1IBX 6-[2,2,2-tris(fluoranyl)ethoxy]pyridine-3-carbothioamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；33 % (w/v) PEG 3,350, 0.1 M HEPES pH 8.0; Inhibitor has been soaked in same condition with addition of 10 % (v/v) DMSO for 24h.
|
Resolution 1.55 Å R-free 0.215 |
| 9FDW Crystal structure of human Sirt2 in complex with a 3-chlorobenzamide-based fragment inhibitor Deposited 2024-05-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | A1IBY 3-chloranyl-~{N}-(pyridin-2-ylmethyl)benzamide × 2 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；31 % (w/v) PEG 3,350, 0.1 M HEPES pH 7.75; Inhibitor has been soaked in same condition with addition of 10 % (v/v) DMSO for 24h.
|
Resolution 1.60 Å R-free 0.214 |
| 9FDX Crystal structure of human Sirt2 in complex with the peptide-based inhibitor KT9 Deposited 2024-05-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 DMS DIMETHYL SULFOXIDE × 3 EDO 1,2-ETHANEDIOL × 2 A1IBZ (2~{S})-2-acetamido-~{N}-[(2~{S},3~{R})-1-azanyl-3-oxidanyl-1-oxidanylidene-butan-2-yl]-6-[[(3~{R})-3-(3,4-dichlorophenyl)sulfanylbutanoyl]amino]hexanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；29 % (w/v) PEG 3,350, 0.1 M HEPES pH 7.25; Inhibitor has been soaked in same condition with addition of 10 % (v/v) DMSO for 24h.
|
Resolution 1.55 Å R-free 0.206 |
| 9FRU Crystal structure of human Sirt2 in complex with a pyrazole-based fragment inhibitor and NAD+ Deposited 2024-06-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 A1IBW [2-[2-methyl-5-(trifluoromethyl)pyrazol-3-yl]phenyl]methanol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；28 % (w/v) PEG 3,350, 0.1 M HEPES pH 7.5; Inhibitor and NAD+ have been soaked in same condition with addition of 10 % (v/v) DMSO for 1h.
|
Resolution 2.00 Å R-free 0.229 |
| 9S1Z Crystal structure of human SIRT2 in complex with the covalent adduct of SirReal-triazole inhibitor Mz242 and ADP-ribose Deposited 2025-07-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | A1JK7 [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S})-5-[5-[[3-[[2-[2-(4,6-dimethylpyrimidin-2-yl)sulfanylethanoylamino]-1,3-thiazol-5-yl]methyl]phenoxy]methyl]-3-(2-methoxyethyl)-1$l^{4},2,3-triazacyclopenta-1,4-dien-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 BU3 (R,R)-2,3-BUTANEDIOL × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of the SIRT2-Mz242-ADPR complex (14.0 mg/mL SIRT2, 10 mM NAD+, 0.5 mM Mz242 with 5 % (v/v) final DMSO concentration) formed after three days, with a reservoir solution containing 24 % (w/v) PEG MME 2000 in 0.1 M Bis-Tris at pH 6.5.
|
Resolution 1.10 Å R-free 0.177 |
| 9S20 Crystal structure of human SIRT2 in complex with SirReal-triazole inhibitor SH10 Deposited 2025-07-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 BU3 (R,R)-2,3-BUTANEDIOL × 2 EDO 1,2-ETHANEDIOL × 1 A1JK0 2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-~{N}-[5-[[3-[[1-[[4-(2-morpholin-4-ylethoxy)phenyl]methyl]-1,2,3-triazol-4-yl]methoxy]phenyl]methyl]-1,3-thiazol-2-yl]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of the SIRT2-SH10 complex (18.0 mg/mL SIRT2, 10 mM NAD+, 1.67 mM of SH10 with 1.67 % (v/v) final DMSO concentration) formed after two days in wells of protein solution and reservoir solution containing 19 % (w/v) PEG 3350 in 0.1 M Bis-Tris at pH 6.5.
|
Resolution 1.50 Å R-free 0.182 |
| 9S21 Crystal structure of human SIRT2 in complex with SirReal-triazole inhibitor LG023 Deposited 2025-07-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 A1JK1 2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-~{N}-[5-[[3-(1~{H}-1,2,3-triazol-4-ylmethoxy)phenyl]methyl]-1,3-thiazol-2-yl]ethanamide × 1 BU3 (R,R)-2,3-BUTANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of the SIRT2-LG023 complex (11.4 mg/mL SIRT2, 3.33 mM of LG023 with 3.33 % (v/v) final DMSO concentration) formed after one day via microseed matrix screening using crystals from the SIRT2-Mz242 complex (PDB 8OWZ) in wells with equal volume of protein solution and reservoir solution containing 32% (w/v) PEG MME 2000 in 0.1 M Bis-Tris at pH 6.5.
|
Resolution 1.55 Å R-free 0.204 |
| 9S22 Crystal structure of human SIRT2 in complex with the covalent adduct of SirReal-triazole inhibitor LG023 and ADP-ribose Deposited 2025-07-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 A1JK2 [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S})-5-[5-[[3-[[2-[2-(4,6-dimethylpyrimidin-2-yl)sulfanylethanoylamino]-1,3-thiazol-5-yl]methyl]phenoxy]methyl]-1,2,3-triazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of the SIRT2-[LG023-ADPR] complex (11.4 mg/mL SIRT2, 10 mM NAD+, 3.33 mM of compound LG023 with 3.33 % (v/v) final DMSO concentration) formed after three days, with a reservoir solution containing 25 % (w/v) PEG 3350 and 0.2 M MgCl2 x 6H2O in 0.1 M Tris at pH 8.5.
|
Resolution 1.95 Å R-free 0.214 |
| 9S23 Crystal structure of human SIRT2 in complex with peptide triazole inhibitor OTDi1 Deposited 2025-07-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 A1JK5 4-dodecyl-1-ethyl-1,2,3-triazole × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of the SIRT2-OTDi1 complex (11.0 mg/mL SIRT2, 5 mM of OTDi1 with 2.5 % (v/v) final DMSO concentration) formed after one day in wells with an equal volume of protein solution and reservoir solution containing 21.5 % (w/v) PEG 3350 in 0.1 M Bis-Tris at pH 6.7.
|
Resolution 2.30 Å R-free 0.259 |
| 9S24 Crystal structure of human SIRT2 in complex with the covalent adduct of peptide triazole inhibitor OTDi1 and ADP-ribose Deposited 2025-07-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 A1JK4 [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S})-5-(5-dodecyl-3-ethyl-1,2,3$l^{4}-triazacyclopenta-2,4-dien-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of the SIRT2-[OTDi1-ADPR] complex (11.0 mg/mL SIRT2, 20 mM NAD+, 5 mM of OTDi1 with 2.5 % (v/v) final DMSO concentration) formed after one day in wells with an equal volume of protein solution and reservoir solution containing 26.5 % (w/v) PEG 3350 in 0.1 M HEPES at pH 7.5.
|
Resolution 2.10 Å R-free 0.229 |
| 9S25 Crystal structure of human SIRT2 in complex with peptide triazole inhibitor LTDi1 Deposited 2025-07-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 A1JK3 4-dodecyl-1-propyl-1,2,3-triazole × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of the SIRT2-LDTi1 complex (11.0 mg/mL SIRT2, 5 mM of LTDi1 with 2.5 % (v/v) final DMSO concentration) formed after one day in wells with an equal volume of protein solution and reservoir solution containing 31.5 % (w/v) PEG 3350 in 0.1 M HEPES at pH 7.5.
|
Resolution 2.10 Å R-free 0.226 |
| 9S26 Crystal structure of human SIRT2 in complex with the covalent adduct of peptide triazole inhibitor LTDi1 and ADP-ribose Deposited 2025-07-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
56–356（301 aa）
Fragment：UNP residues 56-356
|
Not recorded | ZN ZINC ION × 1 A1JK8 [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S})-5-(5-dodecyl-3-propyl-1,2,3$l^{4}-triazacyclopenta-2,4-dien-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Crystals of the SIRT2-[LTDi1-ADPR] complex (11.0 mg/mL SIRT2, 20 mM NAD+, 5 mM of LTDi1 with 2.5 % (v/v) final DMSO concentration) formed after one day in wells with protein solution and reservoir solution containing 29 % (w/v) PEG 3350 and 0.1 M HEPES at pH 7.5.
|
Resolution 2.30 Å R-free 0.252 |
| 9S44 Human Histone Deacetylase SIRT2 Deposited 2025-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2 M ammonium formate
20 % (w/v) PEG3350
|
Resolution 2.15 Å R-free 0.274 |
| 9S46 Human SIRT2 in Complex with RW-78 Deposited 2025-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
|
Not recorded | A1JLK ~{N}-[2-chloranyl-4-[[3-[2-(4,6-dimethylpyrimidin-2-yl)sulfanylethanoylamino]phenyl]methoxy]phenyl]-1-methyl-pyrazole-4-carboxamide × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M sodium acetate
17 % (w/v) PEG3350
|
Resolution 1.45 Å R-free 0.190 |
| 9S48 Human SIRT2 in Complex with RW-80 Deposited 2025-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
56–356（301 aa）
|
Not recorded | ZN ZINC ION × 1 A1JLL ~{N}-[4-[[3-[2-(4,6-dimethylpyrimidin-2-yl)sulfanylethanoylamino]phenyl]methoxy]-2-iodanyl-phenyl]-1-methyl-pyrazole-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 7 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.1 M sodium acetate
17 % (w/v) PEG 3350
|
Resolution 1.45 Å R-free 0.187 |
| 9V7W SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 3 Deposited 2025-05-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
50–356（307 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 8 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 GOL GLYCEROL × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 1.86 Å R-free 0.231 |
| 9VEM SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 1 Deposited 2025-06-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
52–355（304 aa）
|
Not recorded | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 2.57 Å R-free 0.264 |
| 9VEW SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 2 Deposited 2025-06-10 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
52–355（304 aa）
|
Not recorded | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 2.68 Å R-free 0.251 |
| 9VG0 SIRT2 structure in complex with H3K18myr peptide Deposited 2025-06-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
50–356（307 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 5 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 1.61 Å R-free 0.231 |
| 9VG3 SIRT2 structure in complex with H3K18myr peptide: pre NAD binding state Deposited 2025-06-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
57–356（300 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；Tris 8.0, 25% PEG2000MME
|
Resolution 2.15 Å R-free 0.251 |
| 9VGE SIRT2 demyristoylation intermediate I structure Deposited 2025-06-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
50–356（307 aa）
|
Not recorded | NCA NICOTINAMIDE × 1 GOL GLYCEROL × 1 ZN ZINC ION × 1 YDD [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 2.56 Å R-free 0.282 |
| 9VGZ SIRT2-F96A structure in complex with H3K18myr peptide and native NAD Deposited 2025-06-15 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
50–356（307 aa）
|
Mutation：F96A | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 2.34 Å R-free 0.236 |
| 9VH0 SIRT2-H187A structure in complex with H3K18myr peptide and native NAD Deposited 2025-06-16 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
54–355（302 aa）
|
Mutation：H187A | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；0.1 M MES 5.5, 9.2% PEG10000
|
Resolution 2.41 Å R-free 0.273 |
| 9VH0 SIRT2-H187A structure in complex with H3K18myr peptide and native NAD Deposited 2025-06-16 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
54–355（302 aa）
|
Mutation：H187A | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；0.1 M MES 5.5, 9.2% PEG10000
|
Resolution 2.41 Å R-free 0.273 |
77 other PDB entries and 97 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | SIR2_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–293； UniProt 52–356 |
