Research workbench
SIR2-deacetylated peptide (from enzymatic turnover in crystal)
Analyse SIR2-deacetylated peptide (from enzymatic turnover in crystal) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H4J
- Type
- protein
- Length
- 247 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent deacetylase; Cellular tumor antigen P53
- EC
- 3.5.1.-
- UniProt
- Q9WYW0, P04637
- Ligands
- NCA, OAD, ZN
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent deacetylase (EC 3.5.1.-) | protein | 236 | 42% helix, 20% strand | Q9WYW0 |
| D | Cellular tumor antigen P53 | protein | 11 | 0% helix, 27% strand | P04637 |
Ligands and binding sites
- NCA · Nicotinamide · ligand · chains A
- OAD · 2'-O-acetyl adenosine-5-diphosphoribose · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.69 | 0.84 | 34 | NCA, OAD |
Interfaces
1 interface between chains.
- A–D · 514 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2H4J · Sir2-deacetylated peptide (from enzymatic turnover in crystal) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WYW0 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase (Q9WYW0) · 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 Q9WYW0
- Every structure of UniProt P04637
- Elsewhere: RCSB PDB 2H4J · PDBe 2H4J · UniProt Q9WYW0 · UniProt P04637
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