Research workbench
Sirtuin 2 protein with H3K18 myristoylated peptide and intact NAD molecule
Analyse Sirtuin 2 protein with H3K18 myristoylated peptide and intact NAD molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L66
- Type
- protein
- Length
- 304 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.169
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- NAD-dependent protein deacetylase sirtuin-2; Pro-arg-lys-gln-leu-ala
- EC
- 2.3.1.286
- UniProt
- Q8IXJ6
- Ligands
- NAD, 3LX, ZN
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.169 · 2 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-2 (EC 2.3.1.286) | protein | 298 | 37% helix, 18% strand | Q8IXJ6 |
| C | Pro-arg-lys-gln-leu-ala | protein | 6 | 0% helix, 50% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A, C
- 3LX · tridecanethial · ligand · chains A, C
- ZN · Zinc ion · metal · 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 | 510 | 0.85 | 0.91 | 54 | NAD, 3LX |
| 2 | 81 | 0.32 | 0.74 | 18 | empty |
| 3 | 61 | 0.30 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–C · 534 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6L66 · Sirtuin 2 protein with H3K18 myristoylated peptide and intact NAD molecule · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IXJ6 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-2 (Q8IXJ6) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8IXJ6
- Elsewhere: RCSB PDB 6L66 · PDBe 6L66 · UniProt Q8IXJ6
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