MolNFT v1 · #98056 · protein
Structure of NAD-dependent protein deacetylase sirtuin-1 (closed state, 1.85 a)
4KXQ: “Structure of NAD-dependent protein deacetylase sirtuin-1 (closed state, 1.85 a)”. X-ray diffraction, 2 ligands (APR, ZN), 2 pockets (best druggability 0.79). MolNFT v1 #98056 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4KXQ
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-1
- EC
- 3.5.1.-
- UniProt
- Q96EB6
- Ligands
- APR, ZN
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-1 (EC 3.5.1.-) | protein | 279 | 38% helix, 17% strand | Q96EB6 |
| B | NAD-dependent protein deacetylase sirtuin-1 | protein | 26 | 12% helix, 23% strand | Q96EB6 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · chains A
- ZN · Zinc ion · metal · chains A
- BME · Beta-mercaptoethanol · additive · chains A
- GOL · Glycerol · 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 | 425 | 0.79 | 0.88 | 57 | APR, GOL |
| 2 | 134 | 0.40 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 758 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4KXQ · Structure of NAD-dependent protein deacetylase sirtuin-1 (closed state, 1.85 A) · the same entry in another collection · chain A against A, TM-score 1.00
- Q96EB6 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-1 (Q96EB6) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q96EB6
- Elsewhere: RCSB PDB 4KXQ · PDBe 4KXQ · UniProt Q96EB6
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