Research workbench
Human SIRT6 in complex with activator UBCS039
Analyse Human SIRT6 in complex with activator UBCS039 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MF6
- Type
- protein
- Length
- 557 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, 7M2, ZN, SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 16% 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 | 275 | 31% helix, 17% 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
- 7M2 · (4~{R})-4-pyridin-3-yl-4,5-dihydropyrrolo[1,2-a]quinoxaline · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.77 | 0.85 | 52 | AR6, PGE, 7M2 |
| 2 | 444 | 0.76 | 0.85 | 56 | AR6, EDO, 7M2 |
| 3 | 98 | 0.75 | 0.97 | 23 | SO4 |
| 4 | 428 | 0.62 | 0.77 | 54 | SO4 |
| 5 | 178 | 0.53 | 0.79 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1088 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5MF6 · Human Sirt6 in complex with activator UBCS039 · 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 5MF6 · PDBe 5MF6 · UniProt Q8N6T7
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