Research workbench
Crystal structure of human SIRT3 in complex with fluor-de-lys peptide and piceatannol
Analyse Crystal structure of human SIRT3 in complex with fluor-de-lys peptide and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HD8
- Type
- protein
- Length
- 264 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-3, mitochondrial; Fluor-de-lys peptide
- EC
- 3.5.1.-
- UniProt
- Q9NTG7
- Ligands
- PIT, ZN
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 260 | 41% helix, 18% strand | Q9NTG7 |
| F | Fluor-de-lys peptide | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- PIT · Piceatannol · ligand · chains A, F
- ZN · Zinc ion · metal · chains A
- IPA · Isopropyl alcohol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.71 | 0.79 | 46 | empty |
| 2 | 124 | 0.40 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–F · 453 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 4HD8 · Crystal structure of human Sirt3 in complex with Fluor-de-Lys peptide and piceatannol · 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 0.97
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
- Elsewhere: RCSB PDB 4HD8 · PDBe 4HD8 · UniProt Q9NTG7
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