NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 1–399 | Not recorded | Active regulator of SIRT1 × 1 （Q86WX3） ZN ZINC ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；12 % PEG 8.000, 0.1 M HEPES pH 7.5 and 0.2 M NaCl | Resolution 3.27 Å R-free 0.261 |
| 2 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain B； UniProt 1–399 | Not recorded | Active regulator of SIRT1 × 1 （Q86WX3） ZN ZINC ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；12 % PEG 8.000, 0.1 M HEPES pH 7.5 and 0.2 M NaCl | Resolution 3.27 Å R-free 0.261 |
| 3 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain C； UniProt 1–399 | Not recorded | Active regulator of SIRT1 × 1 （Q86WX3） ZN ZINC ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；12 % PEG 8.000, 0.1 M HEPES pH 7.5 and 0.2 M NaCl | Resolution 3.27 Å R-free 0.261 |
| 4 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain D； UniProt 1–399 | Not recorded | Active regulator of SIRT1 × 1 （Q86WX3） ZN ZINC ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；12 % PEG 8.000, 0.1 M HEPES pH 7.5 and 0.2 M NaCl | Resolution 3.27 Å R-free 0.261 |
| 5 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain E； UniProt 1–399 | Not recorded | Active regulator of SIRT1 × 1 （Q86WX3） ZN ZINC ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；12 % PEG 8.000, 0.1 M HEPES pH 7.5 and 0.2 M NaCl | Resolution 3.27 Å R-free 0.261 |
| 6 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain F； UniProt 1–399 | Not recorded | Active regulator of SIRT1 × 1 （Q86WX3） ZN ZINC ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；12 % PEG 8.000, 0.1 M HEPES pH 7.5 and 0.2 M NaCl | Resolution 3.27 Å R-free 0.261 |
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 8BBK | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 3GLR Crystal Structure of human SIRT3 with acetyl-lysine AceCS2 peptide Deposited 2009-03-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
118–399（282 aa）
Fragment：Human SIRT3, residues 118-399
|
Not recorded | ZN ZINC ION × 2 SO4 SULFATE ION × 4 BCT BICARBONATE ION × 2 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 15% (w/v) PEG 12000 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.80 Å R-free 0.226 |
| 3GLS Crystal Structure of Human SIRT3 Deposited 2009-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
118–399（282 aa）
Fragment：Human SIRT3, residues 118-399
|
Mutation：residues 118-399 | ZN ZINC ION × 1 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.70 Å R-free 0.244 |
| 3GLS Crystal Structure of Human SIRT3 Deposited 2009-03-12 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
118–399（282 aa）
Fragment：Human SIRT3, residues 118-399
|
Mutation：residues 118-399 | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.70 Å R-free 0.244 |
| 3GLS Crystal Structure of Human SIRT3 Deposited 2009-03-12 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
118–399（282 aa）
Fragment：Human SIRT3, residues 118-399
|
Mutation：residues 118-399 | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.70 Å R-free 0.244 |
| 3GLS Crystal Structure of Human SIRT3 Deposited 2009-03-12 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
118–399（282 aa）
Fragment：Human SIRT3, residues 118-399
|
Mutation：residues 118-399 | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.70 Å R-free 0.244 |
| 3GLS Crystal Structure of Human SIRT3 Deposited 2009-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
118–399（282 aa）
Fragment：Human SIRT3, residues 118-399
|
Mutation：residues 118-399 | ZN ZINC ION × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.70 Å R-free 0.244 |
| 3GLS Crystal Structure of Human SIRT3 Deposited 2009-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
118–399（282 aa）
Fragment：Human SIRT3, residues 118-399
|
Mutation：residues 118-399 | ZN ZINC ION × 1 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 25% (w/v) PEG 3350 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.70 Å R-free 0.244 |
| 3GLT Crystal Structure of Human SIRT3 with ADPR bound to the AceCS2 peptide containing a thioacetyl lysine Deposited 2009-03-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
118–399（282 aa）
Fragment：Human SIRT3, residues 118-399
|
Not recorded | ZN ZINC ION × 1 SO4 SULFATE ION × 1 CO3 CARBONATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 17% w/v PEG 12000 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.228 |
| 3GLU Crystal Structure of Human SIRT3 with AceCS2 peptide Deposited 2009-03-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
118–399（282 aa）
Fragment：Human SIRT3, residues 118-399
|
Not recorded | SO4 SULFATE ION × 4 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M lithium sulfate monohydrate, 17% w/v PEG 12000 and 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.50 Å R-free 0.248 |
| 4BN4 Structure of human SIRT3 in complex with ADP-ribose Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–399（284 aa）
Fragment：RESIDUES 116-399
|
Not recorded | ZN ZINC ION × 1 NA SODIUM 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 OP2 2-[2-[2-[2-[2-(2-hydroxyethyloxy)ethoxy]ethoxy]ethoxy]ethoxy]ethanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
30% (V/V) PEG600, 5%(W/V) PEG1000, 10% (V/V) GLYCEROL, 0.1 M MES, PH 6.0
|
Resolution 1.30 Å R-free 0.179 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
119–399（281 aa）
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE
|
Resolution 3.25 Å R-free 0.265 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain J
119–399（281 aa）
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE
|
Resolution 3.25 Å R-free 0.265 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 11 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain K
119–399（281 aa）
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE
|
Resolution 3.25 Å R-free 0.265 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 12 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain L
119–399（281 aa）
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE
|
Resolution 3.25 Å R-free 0.265 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
119–399（281 aa）
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE
|
Resolution 3.25 Å R-free 0.265 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
119–399（281 aa）
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE
|
Resolution 3.25 Å R-free 0.265 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
119–399（281 aa）
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE
|
Resolution 3.25 Å R-free 0.265 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
119–399（281 aa）
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE
|
Resolution 3.25 Å R-free 0.265 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
119–399（281 aa）
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE
|
Resolution 3.25 Å R-free 0.265 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain G
119–399（281 aa）
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE
|
Resolution 3.25 Å R-free 0.265 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain H
119–399（281 aa）
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE
|
Resolution 3.25 Å R-free 0.265 |
| 4BN5 Structure of human SIRT3 in complex with SRT1720 inhibitor Deposited 2013-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain I
119–399（281 aa）
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SR7 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE
|
Resolution 3.25 Å R-free 0.265 |
| 4BV3 CRYSTAL STRUCTURE OF SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND NAD Deposited 2013-06-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–399（284 aa）
Fragment：RESIDUES 116-399
|
Not recorded | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 APR ADENOSINE-5-DIPHOSPHORIBOSE × 1 OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 ZN ZINC ION × 1 NO3 NITRATE ION × 1 GOL GLYCEROL × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.2 M (NH4)2SO4, 20% PEG 3350
|
Resolution 2.00 Å R-free 0.209 |
| 4BVB CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND ADP-RIBOSE Deposited 2013-06-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–399（284 aa）
|
Not recorded | OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 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 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.08 M KH2PO4 18 % PEG 8000 20% GLYCEROL
|
Resolution 2.00 Å R-free 0.232 |
| 4BVE CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE FORMED FROM THIO-ACETYL-LYSINE ACS2-PEPTIDE Deposited 2013-06-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–399（284 aa）
Fragment：RESIDUES 116-399
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.6；25% PEG 3350, 0.2 M LISO4, 0.1 M NA CITRATE PH 5.6
|
Resolution 2.05 Å R-free 0.208 |
| 4BVE CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE FORMED FROM THIO-ACETYL-LYSINE ACS2-PEPTIDE Deposited 2013-06-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–399（284 aa）
Fragment：RESIDUES 116-399
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.6；25% PEG 3350, 0.2 M LISO4, 0.1 M NA CITRATE PH 5.6
|
Resolution 2.05 Å R-free 0.208 |
| 4BVF CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE FORMED FROM THIO-ACETYL-LYSINE ACS2-PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX-527 Deposited 2013-06-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–399（284 aa）
Fragment：;RESIDUES 116-399'
;
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.6；25% PEG 3350, 0.2 M LISO4, 0.1 M NA CITRATE PH 5.6
|
Resolution 2.70 Å R-free 0.230 |
| 4BVF CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE FORMED FROM THIO-ACETYL-LYSINE ACS2-PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX-527 Deposited 2013-06-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–399（284 aa）
Fragment：;RESIDUES 116-399'
;
|
Not recorded | ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.6；25% PEG 3350, 0.2 M LISO4, 0.1 M NA CITRATE PH 5.6
|
Resolution 2.70 Å R-free 0.230 |
| 4BVG CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH NATIVE ALKYLIMIDATE FORMED FROM ACETYL-LYSINE ACS2-PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX-527 Deposited 2013-06-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–399（284 aa）
Fragment：RESIDUES 116-399
|
Not recorded | EDO 1,2-ETHANEDIOL × 7 GOL GLYCEROL × 3 SO4 SULFATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 1 XYQ (2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL ACETATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.5；293 K；0.2 M (NH4)2SO4, 0.1M BISTRIS PH 5.5, 21% PEG 3350
|
Resolution 2.50 Å R-free 0.248 |
| 4BVH CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND 2'-O-ACETYL-ADP-RIBOSE Deposited 2013-06-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–399（284 aa）
Fragment：RESIDUES 116-399
|
Not recorded | OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1 ZN ZINC ION × 1 NA SODIUM ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；20% PEG 6000, 0.1 M HEPES PH7
|
Resolution 1.90 Å R-free 0.226 |
| 4BVH CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND 2'-O-ACETYL-ADP-RIBOSE Deposited 2013-06-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
116–399（284 aa）
Fragment：RESIDUES 116-399
|
Not recorded | OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 ZN ZINC ION × 1 CL CHLORIDE 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 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；20% PEG 6000, 0.1 M HEPES PH7
|
Resolution 1.90 Å R-free 0.226 |
| 4BVH CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND 2'-O-ACETYL-ADP-RIBOSE Deposited 2013-06-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
116–399（284 aa）
Fragment：RESIDUES 116-399
|
Not recorded | OCZ (1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide × 1 OAD 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；20% PEG 6000, 0.1 M HEPES PH7
|
Resolution 1.90 Å R-free 0.226 |
| 4C78 Complex of human Sirt3 with Bromo-Resveratrol and ACS2 peptide Deposited 2013-09-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–399（284 aa）
Fragment：RESIDUES 116-399
|
Not recorded | BVB 5-[(E)-2-(4-bromophenyl)ethenyl]benzene-1,3-diol × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；250 MM (NH4)2SO4, 100 MM BISTRIS PH 6, 21% (W/V) PEG 3350
|
Resolution 2.00 Å R-free 0.241 |
| 4C7B Complex of human Sirt3 with Bromo-Resveratrol and Fluor-De-Lys peptide Deposited 2013-09-20 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
117–399（283 aa）
Fragment：RESIDUES 117-399
|
Not recorded | ZN ZINC ION × 1 BVB 5-[(E)-2-(4-bromophenyl)ethenyl]benzene-1,3-diol × 1 IPA ISOPROPYL ALCOHOL × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；200 MM NACL,100 MM HEPES PH 7, 10% (V/V) ISOPROPANOL
|
Resolution 2.10 Å R-free 0.234 |
| 4FVT Human SIRT3 bound to Ac-ACS peptide and Carba-NAD Deposited 2012-06-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
122–395（274 aa）
Fragment：UNP residues 122-395
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SO4 SULFATE ION × 3 ZN ZINC ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.3；291 K；0.2M lithium sulfate monohydrate, 15% (w/v) poly-ethylene glycol (PEG) 12000, and 0.1 M Bis-Tris, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.47 Å R-free 0.249 |
| 4FZ3 Crystal structure of SIRT3 in complex with acetyl p53 peptide coupled with 4-amino-7-methylcoumarin Deposited 2012-07-06 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
118–399（282 aa）
Fragment：residues 118-399
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；0.85M HEPES-NA, 8.5%(V/V) ISO-PROPANOL, 17%(W/V) PEG4000, 15%(V/V) GLYCEROL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
|
Resolution 2.10 Å R-free 0.282 |
| 4HD8 Crystal structure of human Sirt3 in complex with Fluor-de-Lys peptide and piceatannol Deposited 2012-10-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–399（284 aa）
Fragment：UNP residues 116-399
|
Not recorded | ZN ZINC ION × 1 PIT PICEATANNOL × 1 IPA ISOPROPYL ALCOHOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；200 mM NaCl, 100 mM HEPES pH 7, 10% (v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.240 |
| 4JSR Crystal Structure of human SIRT3 with ELT inhibitor 11c [N-{2-[1-(6-carbamoylthieno[3,2-d]pyrimidin-4-yl)piperidin-4-yl]ethyl}-N'-ethylthiophene-2,5-dicarboxamide] Deposited 2013-03-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
118–399（282 aa）
Fragment：UNP residues 118-399
|
Not recorded | ZN ZINC ION × 1 1NQ N-{2-[1-(6-carbamoylthieno[3,2-d]pyrimidin-4-yl)piperidin-4-yl]ethyl}-N'-ethylthiophene-2,5-dicarboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291.15 K；0.1M Tris pH 8.0, 20% PEG 4000 or 20% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
|
Resolution 1.70 Å R-free 0.228 |
| 4JT8 Crystal Structure of human SIRT3 with ELT inhibitor 28 [4-(4-{2-[(2,2-dimethylpropanoyl)amino]ethyl}piperidin-1-yl)thieno[3,2-d]pyrimidine-6-carboxamide[ Deposited 2013-03-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
118–399（282 aa）
Fragment：UNP residues 118-399
|
Not recorded | ZN ZINC ION × 1 1NR 4-(4-{2-[(2,2-dimethylpropanoyl)amino]ethyl}piperidin-1-yl)thieno[3,2-d]pyrimidine-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.26 Å R-free 0.241 |
| 4JT9 Crystal Structure of human SIRT3 with ELT inhibitor 3 [14-(4-{2-[(methylsulfonyl)amino]ethyl}piperidin-1-yl)thieno[3,2-d]pyrimidine-6-carboxamide] Deposited 2013-03-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
118–399（282 aa）
Fragment：UNP residues 118-399
|
Not recorded | ZN ZINC ION × 1 1NS 4-(4-{2-[(methylsulfonyl)amino]ethyl}piperidin-1-yl)thieno[3,2-d]pyrimidine-6-carboxamide × 1 GOL GLYCEROL × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.24 Å R-free 0.247 |
| 4O8Z Crystal structure of human SIRT3 in complex with compound (2-butylbenzofuran-3-yl)(4-(2-(diethylamino)ethoxy)-3,5-diiodophenyl)methanone Deposited 2013-12-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–399（284 aa）
Fragment：UNP RESIDUES 116-399
|
Not recorded | ZN ZINC ION × 1 BBI (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.00 Å R-free 0.204 |
| 5BWN Crystal Structure of SIRT3 with a H3K9 Peptide Containing a Myristoyl Lysine Deposited 2015-06-08 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
118–399（282 aa）
Fragment：UNP RESIDUES 118-399
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2M Ammonium tartrate dibasic (pH 7.0), 20% w/v PEG 3350, 0.01M Urea
|
Resolution 1.94 Å R-free 0.275 |
| 5BWO Crystal Structure of Human SIRT3 in Complex with a Palmitoyl H3K9 Peptide Deposited 2015-06-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
118–399（282 aa）
Fragment：UNP RESIDUES 118-399
|
Not recorded | PLM PALMITIC ACID × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2M Ammonium formate, 20% PEG 3350
|
Resolution 2.38 Å R-free 0.287 |
| 5D7N Crystal structure of human Sirt3 at an improved resolution Deposited 2015-08-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
118–395（278 aa）
Fragment：UNP residues 118-395
|
Not recorded | ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 3 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M magnesium chloride, 25 % (w/v) PEG 3350
|
Resolution 1.83 Å R-free 0.203 |
| 5D7N Crystal structure of human Sirt3 at an improved resolution Deposited 2015-08-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
118–395（278 aa）
Fragment：UNP residues 118-395
|
Not recorded | ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M magnesium chloride, 25 % (w/v) PEG 3350
|
Resolution 1.83 Å R-free 0.203 |
| 5D7N Crystal structure of human Sirt3 at an improved resolution Deposited 2015-08-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
118–395（278 aa）
Fragment：UNP residues 118-395
|
Not recorded | ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M magnesium chloride, 25 % (w/v) PEG 3350
|
Resolution 1.83 Å R-free 0.203 |
| 5D7N Crystal structure of human Sirt3 at an improved resolution Deposited 2015-08-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
118–395（278 aa）
Fragment：UNP residues 118-395
|
Not recorded | ZN ZINC ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 1PE PENTAETHYLENE GLYCOL × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M magnesium chloride, 25 % (w/v) PEG 3350
|
Resolution 1.83 Å R-free 0.203 |
| 5D7N Crystal structure of human Sirt3 at an improved resolution Deposited 2015-08-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
118–395（278 aa）
Fragment：UNP residues 118-395
|
Not recorded | ZN ZINC ION × 1 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M magnesium chloride, 25 % (w/v) PEG 3350
|
Resolution 1.83 Å R-free 0.203 |
| 5D7N Crystal structure of human Sirt3 at an improved resolution Deposited 2015-08-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
118–395（278 aa）
Fragment：UNP residues 118-395
|
Not recorded | ZN ZINC ION × 1 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M magnesium chloride, 25 % (w/v) PEG 3350
|
Resolution 1.83 Å R-free 0.203 |
| 5H4D Crystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride Deposited 2016-10-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
121–391（271 aa）
Fragment：UNP residues 121-391
|
Not recorded | ZN ZINC ION × 1 MG MAGNESIUM ION × 1 BBI (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 MCM 7-AMINO-4-METHYL-CHROMEN-2-ONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.1M HEPES sodium pH 7.5, 10%(v/v) 2-Propanol, 20%(w/v) Polyethylene glycol 4,000
|
Resolution 3.21 Å R-free 0.372 |
| 5H4D Crystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride Deposited 2016-10-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
121–391（271 aa）
Fragment：UNP residues 121-391
|
Not recorded | ZN ZINC ION × 1 MG MAGNESIUM ION × 1 BBI (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 MCM 7-AMINO-4-METHYL-CHROMEN-2-ONE × 1 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；0.1M HEPES sodium pH 7.5, 10%(v/v) 2-Propanol, 20%(w/v) Polyethylene glycol 4,000
|
Resolution 3.21 Å R-free 0.372 |
| 5Y4H Human SIRT3 in complex with halistanol sulfate Deposited 2017-08-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
118–399（282 aa）
Fragment：UNP residues 118-399
|
Not recorded | ZN ZINC ION × 1 8QF [(2~{S},3~{S},5~{S},6~{S},8~{S},9~{S},10~{R},13~{R},14~{R},17~{R})-17-[(2~{R})-6,6-dimethylheptan-2-yl]-10,13-dimethyl-2,3-disulfooxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-6-yl] hydrogen sulfate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Potassium phosphate
|
Resolution 2.60 Å R-free 0.269 |
| 5YTK Crystal structure of SIRT3 bound to a leucylated AceCS2 Deposited 2017-11-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain A
121–394（274 aa）
Chain B
121–394（274 aa）
Chain C
121–394（274 aa）
Chain D
121–394（274 aa）
Chain E
121–394（274 aa）
Chain F
121–394（274 aa）
|
Not recorded | ZN ZINC ION × 6 LEU LEUCINE × 6 LYS LYSINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；0.1M MES monohydrate (pH6.2) and 8% PEG 20,000
|
Resolution 2.70 Å R-free 0.237 |
| 5Z93 Crystal Structure of SIRT3 in complex with H3K9bhb peptide Deposited 2018-02-02 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
117–399（283 aa）
Fragment：UNP residues 117-399
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M MES pH 6.5, 25% PEG 1000
|
Resolution 1.95 Å R-free 0.210 |
| 5Z94 Crystal Structure of SIRT3 in complex with H3K4bhb peptide Deposited 2018-02-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
117–399（283 aa）
Fragment：UNP residues 117-399
|
Not recorded | ZN ZINC ION × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Li2SO4, 0.1M sodium citrate, pH 6.0, 19% PEG 3,350
|
Resolution 1.90 Å R-free 0.191 |
| 5Z94 Crystal Structure of SIRT3 in complex with H3K4bhb peptide Deposited 2018-02-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
117–399（283 aa）
Fragment：UNP residues 117-399
|
Not recorded | ZN ZINC ION × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Li2SO4, 0.1M sodium citrate, pH 6.0, 19% PEG 3,350
|
Resolution 1.90 Å R-free 0.191 |
| 5ZGC Crystal Structure of SIRT3 in complex with H4K16bhb peptide Deposited 2018-03-08 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
121–394（274 aa）
Fragment：UNP residues 121-394
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；0.1M Bicine pH 9.0, 10% PEG 6000
|
Resolution 2.90 Å R-free 0.280 |
| 5ZGC Crystal Structure of SIRT3 in complex with H4K16bhb peptide Deposited 2018-03-08 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
121–394（274 aa）
Fragment：UNP residues 121-394
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；0.1M Bicine pH 9.0, 10% PEG 6000
|
Resolution 2.90 Å R-free 0.280 |
| 5ZGC Crystal Structure of SIRT3 in complex with H4K16bhb peptide Deposited 2018-03-08 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
121–394（274 aa）
Fragment：UNP residues 121-394
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；0.1M Bicine pH 9.0, 10% PEG 6000
|
Resolution 2.90 Å R-free 0.280 |
| 5ZGC Crystal Structure of SIRT3 in complex with H4K16bhb peptide Deposited 2018-03-08 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
121–394（274 aa）
Fragment：UNP residues 121-394
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；0.1M Bicine pH 9.0, 10% PEG 6000
|
Resolution 2.90 Å R-free 0.280 |
| 5ZGC Crystal Structure of SIRT3 in complex with H4K16bhb peptide Deposited 2018-03-08 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
121–394（274 aa）
Fragment：UNP residues 121-394
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；0.1M Bicine pH 9.0, 10% PEG 6000
|
Resolution 2.90 Å R-free 0.280 |
| 5ZGC Crystal Structure of SIRT3 in complex with H4K16bhb peptide Deposited 2018-03-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
121–394（274 aa）
Fragment：UNP residues 121-394
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；0.1M Bicine pH 9.0, 10% PEG 6000
|
Resolution 2.90 Å R-free 0.280 |
| 6ISO Human SIRT3 Recognizing H3K4cr Deposited 2018-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
121–394（274 aa）
|
Not recorded | ZN ZINC ION × 1 CRD (2E)-BUT-2-ENAL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；12% PEG4K, 0.1 M sodium malonate, pH 6.5, 5% isopropanol
|
Resolution 2.95 Å R-free 0.275 |
| 6ISO Human SIRT3 Recognizing H3K4cr Deposited 2018-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
121–394（274 aa）
|
Not recorded | ZN ZINC ION × 1 CRD (2E)-BUT-2-ENAL × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；12% PEG4K, 0.1 M sodium malonate, pH 6.5, 5% isopropanol
|
Resolution 2.95 Å R-free 0.275 |
| 6ISO Human SIRT3 Recognizing H3K4cr Deposited 2018-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
121–394（274 aa）
|
Not recorded | ZN ZINC ION × 1 CRD (2E)-BUT-2-ENAL × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；12% PEG4K, 0.1 M sodium malonate, pH 6.5, 5% isopropanol
|
Resolution 2.95 Å R-free 0.275 |
| 6ISO Human SIRT3 Recognizing H3K4cr Deposited 2018-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
121–394（274 aa）
|
Not recorded | ZN ZINC ION × 1 CRD (2E)-BUT-2-ENAL × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；12% PEG4K, 0.1 M sodium malonate, pH 6.5, 5% isopropanol
|
Resolution 2.95 Å R-free 0.275 |
| 6ISO Human SIRT3 Recognizing H3K4cr Deposited 2018-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain K
121–394（274 aa）
|
Not recorded | CRD (2E)-BUT-2-ENAL × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；12% PEG4K, 0.1 M sodium malonate, pH 6.5, 5% isopropanol
|
Resolution 2.95 Å R-free 0.275 |
| 6ISO Human SIRT3 Recognizing H3K4cr Deposited 2018-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
121–394（274 aa）
|
Not recorded | ZN ZINC ION × 1 CRD (2E)-BUT-2-ENAL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；12% PEG4K, 0.1 M sodium malonate, pH 6.5, 5% isopropanol
|
Resolution 2.95 Å R-free 0.275 |
| 8ANC 14-3-3 sigma sirtuin-3 phospho-peptide complex Deposited 2022-08-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
98–108（11 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 6 CA CALCIUM ION × 4 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M Hepes/NaOH pH 7.5, 0.2 M CaCl2, 26% (v/v) PEG 400, 5% (v/v) glycerol, 1 mM TCEP
|
Resolution 1.11 Å R-free 0.146 |
| 8CCW Crystal structure of human Sirt3 in complex with an acetylated HIV1 Tat-46-54 substrate peptide Deposited 2023-01-27 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
118–399（282 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；10 mg/ml human Sirt3-(118-399) in 20 mM Tris/HCl, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP were incubated with 2 mM ac-Tat-46-54 for 60 min at 293.15 K. The complex was crystallized using the sitting-drop vapor-diffusion method at 293.15 K with 100 mM MES, pH 6.0, 30% (w/v) PEG 200, 5% (w/v) PEG 3000 as reservoir solution.
|
Resolution 1.65 Å R-free 0.209 |
| 8CCZ Crystal structure of human Sirt3 in complex with an inhibiting HIV1 Tat-37-59 peptide Deposited 2023-01-28 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
118–399（282 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；10 mg/ml human Sirt3-(118-399) in 20 mM Tris/HCl, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP were incubated with 2 mM Tat-37-59 in 10% (v/v) DMSO for 60 min at 293.15 K. The complex was crystallized using the sitting-drop vapor-diffusion method at 293.15 K with 100 mM CHES, pH 9.0, 20% (w/v) PEG 8000 as reservoir solution.
|
Resolution 1.95 Å R-free 0.276 |
| 8CCZ Crystal structure of human Sirt3 in complex with an inhibiting HIV1 Tat-37-59 peptide Deposited 2023-01-28 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
118–399（282 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；10 mg/ml human Sirt3-(118-399) in 20 mM Tris/HCl, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP were incubated with 2 mM Tat-37-59 in 10% (v/v) DMSO for 60 min at 293.15 K. The complex was crystallized using the sitting-drop vapor-diffusion method at 293.15 K with 100 mM CHES, pH 9.0, 20% (w/v) PEG 8000 as reservoir solution.
|
Resolution 1.95 Å R-free 0.276 |
| 8HLW Crystal structure of SIRT3 in complex with H4K16la peptide Deposited 2022-12-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
119–399（281 aa）
|
Not recorded | ZN ZINC ION × 1 2OP (2S)-2-HYDROXYPROPANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；0.1 M Tris pH 8.5, 25% (w/v) Polyethylene glycol 3350
|
Resolution 2.50 Å R-free 0.243 |
| 8HLY Crystal structure of SIRT3 in complex with H3K23la peptide Deposited 2022-12-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
119–399（281 aa）
|
Not recorded | GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1 2OP (2S)-2-HYDROXYPROPANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M BIS-TRIS pH at 6.5, 28% (w/v) Polyethylene glycol monomethyl ether 2000
|
Resolution 2.00 Å R-free 0.203 |
| 8HN9 Human SIRT3 Recognizing CCNE2K348la peptide Deposited 2022-12-07 | 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 A
122–395（274 aa）
Chain B
122–395（274 aa）
|
Not recorded | ZN ZINC ION × 2 IMD IMIDAZOLE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.8 M succinic acid, pH 7.0, 0.01M Imidazole
|
Resolution 3.70 Å R-free 0.218 |
| 8V15 Human SIRT3 bound to p53-AMC peptide, Carba-NAD, and Honokiol Deposited 2023-11-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
118–399（282 aa）
|
Not recorded | ZN ZINC ION × 1 CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293.15 K；SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M HEPES, pH 7.5 as reservoir. Following formation of the ternary complex, crystals were soaked with carba-NAD (10 mM).
|
Resolution 2.40 Å R-free 0.303 |
| 8V15 Human SIRT3 bound to p53-AMC peptide, Carba-NAD, and Honokiol Deposited 2023-11-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
118–399（282 aa）
|
Not recorded | ZN ZINC ION × 1 CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 Y4T (1P)-3',5-di(prop-2-en-1-yl)[1,1'-biphenyl]-2,4'-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293.15 K；SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M HEPES, pH 7.5 as reservoir. Following formation of the ternary complex, crystals were soaked with carba-NAD (10 mM).
|
Resolution 2.40 Å R-free 0.303 |
| 8V2N Human SIRT3 co-crystallized with ligands, including p53-AMC peptide and Carba-NAD Deposited 2023-11-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
118–399（282 aa）
|
Not recorded | CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293.15 K；SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M HEPES, pH 7.5 as reservoir. Following formation of the ternary complex, crystals were soaked with carba-NAD (10 mM).
|
Resolution 1.74 Å R-free 0.282 |
| 8V5U Human SIRT3 bound to p53-AMC peptide and Honokiol Deposited 2023-12-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
118–399（282 aa）
|
Not recorded | ZN ZINC ION × 1 Y4T (1P)-3',5-di(prop-2-en-1-yl)[1,1'-biphenyl]-2,4'-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293.15 K；SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M HEPES, pH 7.5 as reservoir. Following formation of the ternary complex, crystals were soaked with carba-NAD (10 mM).
|
Resolution 1.48 Å R-free 0.246 |
| 9CBT Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10 Deposited 2024-06-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
118–399（282 aa）
|
Not recorded | ZN ZINC ION × 1 5IA 2-{[(2S)-6-[(Z)-(1-{[(2R,3R,4R,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-4-hydroxy-2-sulfanyloxolan-3-yl]oxy}tetradecylidene)amino]-2-{[(benzyloxy)carbonyl]amino}hexanoyl]amino}-N,N,N-triethylethan-1-aminium (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 7.9, 100 mM MgCl2, 20 % w/v PEG8000, and 17.5 % w/v PEG400
|
Resolution 1.95 Å R-free 0.239 |
| 9CBT Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10 Deposited 2024-06-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
118–399（282 aa）
|
Not recorded | ZN ZINC ION × 1 PG4 TETRAETHYLENE GLYCOL × 1 5I7 (phenylmethyl) ~{N}-[(2~{S})-6-[[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-6-oxidanyl-2-tridecyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]amino]-1-oxidanylidene-1-[2-(triethyl-$l^{4}-azanyl)ethylamino]hexan-2-yl]carbamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；100 mM Tris, pH 7.9, 100 mM MgCl2, 20 % w/v PEG8000, and 17.5 % w/v PEG400
|
Resolution 1.95 Å R-free 0.239 |
| 9KTK Crystal structure of human SIRT3 with its activator SKLB-11A Deposited 2024-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
118–391（274 aa）
Chain B
118–391（274 aa）
Chain C
118–391（274 aa）
Chain D
118–391（274 aa）
|
Not recorded | ZN ZINC ION × 4 A1EHU methyl 2-azanyl-1-[(4-fluorophenyl)methyl]pyrrolo[3,2-b]quinoxaline-3-carboxylate × 4 MG MAGNESIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Li2SO4, 1.1M (NH4)2SO4, 0.1M Tris-HCl pH 7.5
|
Resolution 2.49 Å R-free 0.340 |
| 9KTK Crystal structure of human SIRT3 with its activator SKLB-11A Deposited 2024-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
118–391（274 aa）
Chain D
118–391（274 aa）
|
Not recorded | ZN ZINC ION × 2 A1EHU methyl 2-azanyl-1-[(4-fluorophenyl)methyl]pyrrolo[3,2-b]quinoxaline-3-carboxylate × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Li2SO4, 1.1M (NH4)2SO4, 0.1M Tris-HCl pH 7.5
|
Resolution 2.49 Å R-free 0.340 |
| 9KTK Crystal structure of human SIRT3 with its activator SKLB-11A Deposited 2024-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
118–391（274 aa）
Chain C
118–391（274 aa）
|
Not recorded | ZN ZINC ION × 2 A1EHU methyl 2-azanyl-1-[(4-fluorophenyl)methyl]pyrrolo[3,2-b]quinoxaline-3-carboxylate × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Li2SO4, 1.1M (NH4)2SO4, 0.1M Tris-HCl pH 7.5
|
Resolution 2.49 Å R-free 0.340 |
| 9S27 Crystal structure of human SIRT3 in complex with the covalent adduct of peptide triazole inhibitor LTDi1 and ADP-ribose Deposited 2025-07-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
118–395（278 aa）
Fragment：UNP residues 118-395
|
Not recorded | ZN ZINC ION × 1 BU3 (R,R)-2,3-BUTANEDIOL × 2 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 SIRT3-[LTDi1-ADPR] complex (10.0 mg/mL SIRT3, 15 mM NAD+, 3 mM of LTDi1 with 1.5 % (v/v) final DMSO concentration) formed after 2 days in wells with an equal volume of 300 nL protein solution and 300 nL reservoir solution containing 3 M NaCl in 0.1 M Tris at pH 8.5.
|
Resolution 1.60 Å R-free 0.194 |
43 other PDB entries and 85 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | SIR3_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–399； UniProt 1–399 Author chain B； PDBConstruct 1–399； UniProt 1–399 Author chain C； PDBConstruct 1–399； UniProt 1–399 Author chain D； PDBConstruct 1–399； UniProt 1–399 Author chain E； PDBConstruct 1–399； UniProt 1–399 Author chain F； PDBConstruct 1–399； UniProt 1–399 |
