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9dpi

Cryo-EM structure of SerRS dimer in complex with two SIRT2

Method: ELECTRON MICROSCOPY Dmax: 144.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine--tRNA ligase, cytoplasmic

Homo sapiens

UniProt P49591

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain D； UniProt 1–514 Chain F； UniProt 1–514 Not recorded NAD-dependent protein deacetylase sirtuin-2 × 2 （Q8IXJ6） 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

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 9DPI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3VBB Crystal Structure of Seryl-tRNA Synthetase from Human at 2.9 angstroms Deposited 2012-01-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–514（514 aa）
Chain B 1–514（514 aa）
Not recorded MG MAGNESIUM ION × 2 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 3350, 0.2 M tri-sodium citrate pH 7.0, 5mM ATP, 10mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.89 Å R-free 0.250
3VBB Crystal Structure of Seryl-tRNA Synthetase from Human at 2.9 angstroms Deposited 2012-01-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–514（514 aa）
Chain D 1–514（514 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 3350, 0.2 M tri-sodium citrate pH 7.0, 5mM ATP, 10mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.89 Å R-free 0.250
3VBB Crystal Structure of Seryl-tRNA Synthetase from Human at 2.9 angstroms Deposited 2012-01-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–514（514 aa）
Chain F 1–514（514 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 3350, 0.2 M tri-sodium citrate pH 7.0, 5mM ATP, 10mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.89 Å R-free 0.250
4L87 Crystal structure of the human seryl-tRNA synthetase in complex with Ser-SA at 2.9 Angstrom resolution Deposited 2013-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–477（476 aa） Fragment：UNP residues 2-477
Not recorded SSA 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE × 2 PO4 PHOSPHATE ION × 2 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG3350, 0.2 M ammonium fluoride or ammonium formate, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.90 Å R-free 0.268
4RQE human Seryl-tRNA synthetase dimer complexed with two molecules of tRNAsec Deposited 2014-11-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–514（514 aa）
Chain C 1–514（514 aa）
Mutation：E156T, R157S Mutation：E156T, R157S SER SERINE × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；18%(m/v) PEG3350, 0.1M NaCl, 0.1M Tris-HCl (pH8.0), 0.1M Sodium malonate pH7.0. , VAPOR DIFFUSION, temperature 298K
Resolution 4.00 Å R-free 0.322
4RQF human Seryl-tRNA synthetase dimer complexed with one molecule of tRNAsec Deposited 2014-11-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain A 1–514（514 aa）
Chain B 1–514（514 aa）
Mutation：E447K Mutation：E447K ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 SER SERINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；18%(m/v) PEG3350, 0.1M NaCl, 0.1M Tris-HCl (pH8.0), 0.1M Sodium malonate pH7.0., VAPOR DIFFUSION, temperature 298K
Resolution 3.50 Å R-free 0.314
8P7B CryoEM structure of METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry Deposited 2023-05-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–514（514 aa）
Chain D 1–514（514 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.42 Å
8P7C CryoEM structure of METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry Deposited 2023-05-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–514（514 aa）
Chain D 1–514（514 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8P7D CryoEM structure of METTL6 tRNA SerRS complex in a 1:1:2 stoichiometry Deposited 2023-05-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain B 1–514（514 aa）
Chain D 1–514（514 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9DPD Cryo-EM structure of SerRS dimer in complex with one SIRT2 Deposited 2024-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–514（514 aa）
Chain D 1–514（514 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

8 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SYSC_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain D； PDBConstruct 1–514； UniProt 1–514 Author chain F； PDBConstruct 1–514； UniProt 1–514

NAD-dependent protein deacetylase sirtuin-2

Homo sapiens

UniProt Q8IXJ6

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 1–389 Chain E； UniProt 1–389 Not recorded Serine--tRNA ligase, cytoplasmic × 2 （P49591） 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

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 9DPI 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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 × 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
7BOT Human SIRT2 in complex with myristoyl thiourea inhibitor, No.23 Deposited 2020-03-19 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 × 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；0.15M Potassium bromide, 30% (w/v) Polyethylene glycol monomethyl ether 2000
Resolution 1.70 Å R-free 0.320
7T1D Human SIRT2 in complex with small molecule 359 Deposited 2021-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion 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
9FDR Crystal structure of human Sirt2 in apo form with opened selectivity pocket Deposited 2024-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 2
Chains and sequence ranges Author chain C； PDBConstruct 1–389； UniProt 1–389 Author chain E； PDBConstruct 1–389； UniProt 1–389

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9dpi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9dpi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9dpi
Deposition date deposition_date2024-09-21
Structure title titleCryo-EM structure of SerRS dimer in complex with two SIRT2
Keywords keywordsenzymes, protein complexes, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier40.76 Å
Radius of gyration Rg (electron density) rg_electron40.63 Å
Forward intensity I(0) i0172503000.00
Molecular weight molecular_weight108580.0 kDa
Excluded volume excluded_volume136760 ų
Envelope volume envelope_volume192570 ų
Hydration-shell volume shell_volume42010 ų
Envelope diameter envelope_diameter143.0 Å
Shell Rg shell_rg42.75 Å
Envelope Rg envelope_rg40.07 Å
Shape Rg shape_rg40.65 Å
Total Rg total_rg40.72 Å
Total atoms total_atoms7635
Residues n_residues959
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax144.8 Å
Rg (real space) rg_real41.02 Å
Rg uncertainty (real space) rg_real_error1.56 Å
I(0) (real space) i0_real1.7250e+08
I(0) uncertainty (real space) i0_real_error3.0540e+06
Rg (reciprocal space) rg_reciprocal40.76 Å
I(0) (reciprocal space) i0_reciprocal172500000.0000
Solution quality estimate total_estimate0.8200
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary52.0 Å
Skewness Skewness skewness0.480
Kurtosis Kurtosis kurtosis-0.267
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18550000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.738; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.666; Smooth: 0.775
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)