Research workbench
The structural basis of sirtuin substrate specificity
Analyse The structural basis of sirtuin substrate specificity in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H2H
- Type
- protein
- Length
- 241 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent deacetylase; Histone H4
- EC
- 3.5.1.-
- UniProt
- Q9WYW0, P02309
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent deacetylase (EC 3.5.1.-) | protein | 234 | 42% helix, 21% strand | Q9WYW0 |
| B | Histone H4 | protein | 7 | 0% helix, 43% strand | P02309 |
Ligands and binding sites
- 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 | 211 | 0.64 | 0.83 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 573 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 2H2H · The Structural basis of sirtuin substrate specificity · 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
- P02309 · AlphaFold monomer V2.0 prediction for histone H4 (P02309) · a predicted model of the same protein · chain B against A, TM-score 0.45
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 P02309
- Elsewhere: RCSB PDB 2H2H · PDBe 2H2H · UniProt Q9WYW0 · UniProt P02309
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