MolNFT v1 · #109472 · protein
SIRT2 in complex with a myristoyl peptide
4X3P · NAD-dependent protein deacetylase sirtuin-2: “SIRT2 in complex with a myristoyl peptide”. X-ray diffraction, 3 ligands (CNA, 3LX, ZN), 2 pockets (best druggability 0.85). MolNFT v1 #109472 on GenesisL1: 3D structure, binding sites…
- PDB
- 4X3P
- Type
- protein
- Length
- 302 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-2; Peptide pro-lys-lys-thr-gly
- EC
- 3.5.1.-
- UniProt
- Q8IXJ6
- Ligands
- CNA, 3LX, ZN
- Pockets
- 2 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 297 | 38% helix, 18% strand | Q8IXJ6 |
| C | Peptide pro-lys-lys-thr-gly | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- CNA · Carba-nicotinamide-adenine-dinucleotide · ligand · chains A, C
- 3LX · tridecanethial · ligand · chains A, C
- ZN · Zinc ion · metal · 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
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 | 453 | 0.85 | 0.92 | 52 | CNA, 3LX |
| 2 | 130 | 0.38 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–C · 410 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 4X3P · PDBe 4X3P · UniProt Q8IXJ6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.