MolNFT v1 · #161373 · protein
Human SIRT6 in complex with ADP-ribose and the activator cyanidin
6QCH · NAD-dependent protein deacetylase sirtuin-6: “Human SIRT6 in complex with ADP-ribose and the activator cyanidin”. X-ray diffraction, 4 ligands (AR6, HWB, ZN), 6 pockets (best druggability 0.81). MolNFT v1 #161373 on GenesisL1: 3D…
- PDB
- 6QCH
- Type
- protein
- Length
- 556 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-6
- EC
- 3.5.1.-
- UniProt
- Q8N6T7
- Ligands
- AR6, HWB, ZN, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-6 (EC 3.5.1.-) | protein | 281 | 31% helix, 15% strand | Q8N6T7 |
| B | NAD-dependent protein deacetylase sirtuin-6 (EC 3.5.1.-) | protein | 275 | 30% helix, 16% strand | Q8N6T7 |
Ligands and binding sites
- AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · 2 copies · chains A, B
- HWB · cyanidin · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.81 | 0.86 | 73 | AR6, EDO, HWB, SO4 |
| 2 | 448 | 0.77 | 0.85 | 50 | AR6, HWB |
| 3 | 450 | 0.61 | 0.76 | 52 | SO4 |
| 4 | 181 | 0.55 | 0.80 | 28 | empty |
| 5 | 207 | 0.53 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1080 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6QCH · Human Sirt6 in complex with ADP-ribose and the activator cyanidin · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8N6T7
- Elsewhere: RCSB PDB 6QCH · PDBe 6QCH · UniProt Q8N6T7
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