MolNFT v2 · #212132 · protein
Crystal structure of SIRT3 in complex with H4K16la peptide
8HLW · NAD-dependent protein deacetylase sirtuin-3, mitochondrial: “Crystal structure of SIRT3 in complex with H4K16la peptide”. X-ray diffraction at 2.5, 2 ligands (2OP, ZN), 3 pockets (best druggability 0.69). MolNFT v2 #212132 on…
- PDB
- 8HLW
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- NAD-dependent protein deacetylase sirtuin-3, mitochondrial; Histone H4 residues 20-27
- EC
- 2.3.1.286
- UniProt
- Q9NTG7, P62805
- Ligands
- 2OP, ZN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 2.3.1.286) | protein | 266 | 42% helix, 20% strand | Q9NTG7 |
| B | Histone H4 residues 20-27 | protein | 8 | 0% helix, 38% strand | P62805 |
Ligands and binding sites
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 | 348 | 0.69 | 0.82 | 40 | 2OP |
| 2 | 72 | 0.43 | 0.80 | 19 | empty |
| 3 | 106 | 0.38 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 568 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- P62805 · AlphaFold monomer V2.0 prediction for histone H4 (P62805) · a predicted model of the same protein · chain B against A, TM-score 0.38
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 P62805
- Elsewhere: RCSB PDB 8HLW · PDBe 8HLW · UniProt Q9NTG7 · UniProt P62805
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