MolNFT v1 · #170067 · protein
Human SIRT6 3-318 in complex with ADP-ribose and the activator mdl-801
6XVG · NAD-dependent protein deacetylase sirtuin-6: “Human SIRT6 3-318 in complex with ADP-ribose and the activator mdl-801”. X-ray diffraction, 4 ligands (AR6, 8L9, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #170067 on GenesisL1…
- PDB
- 6XVG
- Type
- protein
- Length
- 1,675 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-6
- EC
- 2.3.1.286
- UniProt
- Q8N6T7
- Ligands
- AR6, 8L9, ZN, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | NAD-dependent protein deacetylase sirtuin-6 (EC 2.3.1.286) | protein | 278 | 30% helix, 15% strand | Q8N6T7 |
| B | NAD-dependent protein deacetylase sirtuin-6 (EC 2.3.1.286) | protein | 284 | 31% helix, 17% strand | Q8N6T7 |
| C | NAD-dependent protein deacetylase sirtuin-6 (EC 2.3.1.286) | protein | 279 | 30% helix, 15% strand | Q8N6T7 |
| D | NAD-dependent protein deacetylase sirtuin-6 (EC 2.3.1.286) | protein | 277 | 31% helix, 16% strand | Q8N6T7 |
| E | NAD-dependent protein deacetylase sirtuin-6 (EC 2.3.1.286) | protein | 279 | 30% helix, 15% 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 · 6 copies · chains A, B, C, E, D, F
- 8L9 · 5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 13 copies · chains A, D, B, C, F, E
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.84 | 0.85 | 124 | AR6, GOL, 8L9, SO4 |
| 2 | 621 | 0.81 | 0.86 | 70 | AR6, 8L9 |
| 3 | 610 | 0.81 | 0.86 | 67 | AR6, 8L9 |
| 4 | 461 | 0.78 | 0.86 | 59 | AR6 |
| 5 | 524 | 0.76 | 0.84 | 56 | AR6, 8L9 |
Interfaces
10 interfaces between chains.
- C–E · 1187 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1174 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1130 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 287 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 241 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6XVG · Human Sirt6 3-318 in complex with ADP-ribose and the activator MDL-801 · 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 6XVG · PDBe 6XVG · UniProt Q8N6T7
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