Research workbench
Crystal structure of human SIRT3 in complex with thioalkylimidate formed from thio-acetyl-lysine ACS2-peptide
Analyse Crystal structure of human SIRT3 in complex with thioalkylimidate formed from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BVE
- Type
- protein
- Length
- 280 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.05
- Source
- HOMO SAPIENS; SYNTHETIC CONSTRUCT
- Molecule
- NAD-dependent protein deacetylase sirtuin-3, mitochondrial; Acetyl-coenzyme a synthetase…
- EC
- 3.5.1.-, 6.2.1.1
- UniProt
- Q9NTG7, Q9NUB1
- Ligands
- ZN, CL, SO4
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.05 · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 274 | 43% helix, 18% strand | Q9NTG7 |
| B | Acetyl-coenzyme a synthetase 2-like, mitochondrial (EC 6.2.1.1) | protein | 6 | 0% helix, 33% strand | Q9NUB1 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.76 | 0.95 | 25 | empty |
| 2 | 69 | 0.40 | 0.79 | 20 | empty |
| 3 | 99 | 0.34 | 0.73 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 954 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 4BVE · Crystal structure of human SIRT3 in complex with thioalkylimidate formed from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NTG7 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-3… · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9NUB1 · AlphaFold monomer V2.0 prediction for acetyl-coenzyme a synthetase 2-like, mitochondrial… · a predicted model of the same protein · chain B against A, TM-score 0.69
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9NTG7
- Every structure of UniProt Q9NUB1
- Elsewhere: RCSB PDB 4BVE · PDBe 4BVE · UniProt Q9NTG7 · UniProt Q9NUB1
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