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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P53686 New Search
12PDB entries
19Biological assembly
21chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1Q14 Structure and autoregulation of the yeast Hst2 homolog of Sir2 Deposited 2003-07-18 Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain A 1–357（357 aa） Fragment：histone/protein deacetylase
Not recorded ZN ZINC ION × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEg4K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.251
1Q17 Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide Deposited 2003-07-18 Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain A 1–294（294 aa） Fragment：protein deacetylase
Chain B 1–294（294 aa） Fragment：protein deacetylase
Chain C 1–294（294 aa） Fragment：protein deacetylase
Not recorded ZN ZINC ION × 3 CL CHLORIDE ION × 4 APR ADENOSINE-5-DIPHOSPHORIBOSE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；(NH4)2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.247
1Q1A Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide Deposited 2003-07-18 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 5–293（289 aa） Fragment：C-terminla deletion of hst2
Not recorded ZN ZINC ION × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；294 K；PEG 4K, , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 1.50 Å R-free 0.210
1SZC Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases Deposited 2004-04-05 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–294（294 aa） Fragment：Catalytic core domain
Not recorded ZN ZINC ION × 1 CL CHLORIDE ION × 1 CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；Ammonium Sulfate, Bis-tris, pH 6.5, VAPOR DIFFUSION, temperature 293K
Resolution 1.75 Å R-free 0.239
1SZC Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases Deposited 2004-04-05 Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 1–294（294 aa） Fragment：Catalytic core domain
Not recorded ZN ZINC ION × 2 CL CHLORIDE ION × 2 CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 GOL GLYCEROL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；Ammonium Sulfate, Bis-tris, pH 6.5, VAPOR DIFFUSION, temperature 293K
Resolution 1.75 Å R-free 0.239
1SZD Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases Deposited 2004-04-05 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–294（294 aa） Fragment：catalytic core domain
Not recorded CL CHLORIDE ION × 1 ZN ZINC ION × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；Ammonium Sulfate, Bis-Tris, pH 6.5, VAPOR DIFFUSION, temperature 293K
Resolution 1.50 Å R-free 0.230
1SZD Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases Deposited 2004-04-05 Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 1–294（294 aa） Fragment：catalytic core domain
Not recorded CL CHLORIDE ION × 2 ZN ZINC ION × 2 APR ADENOSINE-5-DIPHOSPHORIBOSE × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；Ammonium Sulfate, Bis-Tris, pH 6.5, VAPOR DIFFUSION, temperature 293K
Resolution 1.50 Å R-free 0.230
2OD2 Crystal Structure of yHst2 I117F mutant bound to carba-NAD+ and an acetylated H4 peptide Deposited 2006-12-21 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–294（294 aa） Fragment：Hst2 catalytic core domain, residues 1-294
Mutation：I117F ZN ZINC ION × 1 CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；2.0 M Ammonium Sulfate, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.233
2OD2 Crystal Structure of yHst2 I117F mutant bound to carba-NAD+ and an acetylated H4 peptide Deposited 2006-12-21 Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 1–294（294 aa） Fragment：Hst2 catalytic core domain, residues 1-294
Mutation：I117F ZN ZINC ION × 2 CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 GOL GLYCEROL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；2.0 M Ammonium Sulfate, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.233
2OD7 Crystal Structure of yHst2 bound to the intermediate analogue ADP-HPD, and and aceylated H4 peptide Deposited 2006-12-21 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–294（294 aa） Fragment：Hst2 catalytic core domain, residues 1-294
Not recorded ZN ZINC ION × 1 A1R 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；2.0 M Ammonium Sulfate, 0.1 M sodium citrate, 0.2 M potassium/sodium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.234
2OD7 Crystal Structure of yHst2 bound to the intermediate analogue ADP-HPD, and and aceylated H4 peptide Deposited 2006-12-21 Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 1–294（294 aa） Fragment：Hst2 catalytic core domain, residues 1-294
Not recorded ZN ZINC ION × 2 A1R 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；2.0 M Ammonium Sulfate, 0.1 M sodium citrate, 0.2 M potassium/sodium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.234
2OD9 Structural Basis for Nicotinamide Inhibition and Base Exchange in Sir2 Enzymes Deposited 2006-12-21 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–294（294 aa） Fragment：Hst2 catalytic core domain, residues 1-294
Not recorded ZN ZINC ION × 1 A1R 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE × 1 NCA NICOTINAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；2.0 M Ammonium Sulfate, 0.1 M sodium citrate, 0.2 M potassium/sodium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.05 Å R-free 0.245
2OD9 Structural Basis for Nicotinamide Inhibition and Base Exchange in Sir2 Enzymes Deposited 2006-12-21 Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 1–294（294 aa） Fragment：Hst2 catalytic core domain, residues 1-294
Not recorded ZN ZINC ION × 2 A1R 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE × 2 NCA NICOTINAMIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；2.0 M Ammonium Sulfate, 0.1 M sodium citrate, 0.2 M potassium/sodium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.05 Å R-free 0.245
2QQF Hst2 bound to ADP-HPD and Acetylated histone H4 Deposited 2007-07-26 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 1–294（294 aa）
Not recorded ZN ZINC ION × 2 A1R 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；2.0 M Ammonium Sulfate, 100 mM Na citrate and 200 mM K/Na tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.253
2QQF Hst2 bound to ADP-HPD and Acetylated histone H4 Deposited 2007-07-26 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–294（294 aa）
Not recorded ZN ZINC ION × 1 A1R 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；2.0 M Ammonium Sulfate, 100 mM Na citrate and 200 mM K/Na tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.253
2QQG Hst2 bound to ADP-HPD, acetyllated histone H4 and nicotinamide Deposited 2007-07-26 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–294（294 aa）
Not recorded ZN ZINC ION × 1 A1R 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE × 1 NCA NICOTINAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；298 K；2.0 M Ammonium Sulfate, 100 mM Na citrate, pH 5.6, 200 mM K/Na tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.60
Resolution 2.05 Å R-free 0.245
2QQG Hst2 bound to ADP-HPD, acetyllated histone H4 and nicotinamide Deposited 2007-07-26 Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 1–294（294 aa）
Not recorded ZN ZINC ION × 2 A1R 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE × 2 NCA NICOTINAMIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；298 K；2.0 M Ammonium Sulfate, 100 mM Na citrate, pH 5.6, 200 mM K/Na tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.60
Resolution 2.05 Å R-free 0.245
7F4E Crystal structure of Hst2 in complex with H3K9bz peptide Deposited 2021-06-18 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 8–294（287 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；25% (w/v) PEG 1500, 0.1M MMT/Sodium hydroxide
Resolution 1.78 Å R-free 0.216
7F51 Crystal structure of Hst2 in complex with 2'-O-Benzoyl ADP Ribose Deposited 2021-06-21 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 8–294（287 aa）
Not recorded ZN ZINC ION × 1 BA7 [(2R,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] benzoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Ammonium fluoride, 20% w/v Polyethylene glycol 3350
Resolution 1.98 Å R-free 0.220

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.