MolNFT v1 · #38574 · protein
The structural basis of sirtuin substrate affinity
2H2G · NAD-dependent deacetylase: “The structural basis of sirtuin substrate affinity”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.65). MolNFT v1 #38574 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2H2G
- Type
- protein
- Length
- 241 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent deacetylase; Histone H3 peptide
- EC
- 3.5.1.-
- UniProt
- Q9WYW0, P61830
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent deacetylase (EC 3.5.1.-) | protein | 236 | 42% helix, 20% strand | Q9WYW0 |
| B | Histone H3 peptide | protein | 5 | 0% helix, 40% strand | P61830 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · 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 | 200 | 0.65 | 0.84 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 479 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (acetylation).
Compared structures
- 2H2G · The Structural Basis of Sirtuin substrate affinity · 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
- P61830 · AlphaFold monomer V2.0 prediction for histone H3 (P61830) · a predicted model of the same protein · chain B against A, TM-score 0.70
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 P61830
- Elsewhere: RCSB PDB 2H2G · PDBe 2H2G · UniProt Q9WYW0 · UniProt P61830
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