Research workbench
Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr)
Analyse Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y6O
- Type
- protein
- Length
- 567 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- NAD-dependent protein deacetylase sirtuin-2; peptide LEU-PRO-LYS-MYK-THR-GLY-GLY
- EC
- 3.5.1.-
- UniProt
- Q8IXJ6
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · resolution 1.6 · 3 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 277 | 40% helix, 18% strand | Q8IXJ6 |
| B | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 276 | 39% helix, 19% strand | Q8IXJ6 |
| C, D | peptide LEU-PRO-LYS-MYK-THR-GLY-GLY | protein | 7 | 0% helix, 29% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.70 | 0.75 | 65 | empty |
| 2 | 250 | 0.70 | 0.85 | 39 | empty |
| 3 | 156 | 0.68 | 0.88 | 32 | empty |
| 4 | 75 | 0.35 | 0.77 | 16 | empty |
| 5 | 60 | 0.32 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–D · 824 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 820 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 426 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4Y6O · Human SIRT2 in complex with myristoylated peptide (TNF-ALPHAK20MYR) · 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 B against A, TM-score 0.96
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 4Y6O · PDBe 4Y6O · UniProt Q8IXJ6
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