MolNFT v1 · #161370 · protein
Human SIRT6 in complex with ADP-ribose and the activator quercetin
6QCD · NAD-dependent protein deacetylase sirtuin-6: “Human SIRT6 in complex with ADP-ribose and the activator quercetin”. X-ray diffraction, 4 ligands (AR6, QUE, ZN), 7 pockets (best druggability 0.77). MolNFT v1 #161370 on GenesisL1: 3D…
- PDB
- 6QCD
- Type
- protein
- Length
- 559 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, QUE, ZN, SO4
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-6 (EC 3.5.1.-) | protein | 282 | 30% helix, 15% strand | Q8N6T7 |
| B | NAD-dependent protein deacetylase sirtuin-6 (EC 3.5.1.-) | protein | 277 | 32% 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
- QUE · 3,5,7,3',4'-pentahydroxyflavone · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.77 | 0.85 | 57 | AR6, QUE, PGE |
| 2 | 498 | 0.76 | 0.84 | 52 | AR6, QUE, PG4 |
| 3 | 89 | 0.75 | 0.97 | 24 | SO4 |
| 4 | 393 | 0.60 | 0.76 | 53 | SO4 |
| 5 | 203 | 0.55 | 0.79 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1102 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6QCD · Human Sirt6 in complex with ADP-ribose and the activator quercetin · 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 6QCD · PDBe 6QCD · UniProt Q8N6T7
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