Research workbench
Human SIRT6 3-318 in complex with ADP-ribose
Analyse Human SIRT6 3-318 in complex with ADP-ribose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XV6
- Type
- protein
- Length
- 1,702 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, NCA, ZN, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-6 (EC 2.3.1.286) | protein | 288 | 31% helix, 15% strand | Q8N6T7 |
| B | NAD-dependent protein deacetylase sirtuin-6 (EC 2.3.1.286) | protein | 279 | 31% helix, 15% strand | Q8N6T7 |
| C | NAD-dependent protein deacetylase sirtuin-6 (EC 2.3.1.286) | protein | 287 | 30% helix, 15% strand | Q8N6T7 |
| D | NAD-dependent protein deacetylase sirtuin-6 (EC 2.3.1.286) | protein | 280 | 30% helix, 15% strand | Q8N6T7 |
| E | NAD-dependent protein deacetylase sirtuin-6 (EC 2.3.1.286) | protein | 279 | 30% helix, 15% strand | Q8N6T7 |
| F | NAD-dependent protein deacetylase sirtuin-6 (EC 2.3.1.286) | protein | 289 | 31% 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
- NCA · Nicotinamide · 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 · 22 copies · chains A, F, B, C, E, D
- GOL · Glycerol · additive · 8 copies · chains A, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.84 | 0.85 | 132 | SO4, AR6, NCA, GOL |
| 2 | 713 | 0.84 | 0.87 | 94 | AR6, NCA, GOL, SO4 |
| 3 | 744 | 0.78 | 0.82 | 70 | AR6, NCA, SO4 |
| 4 | 518 | 0.77 | 0.84 | 59 | AR6, NCA, GOL |
| 5 | 494 | 0.77 | 0.84 | 59 | AR6, NCA, GOL |
Interfaces
10 interfaces between chains.
- C–E · 1246 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1154 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1153 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 374 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 301 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6XV6 · Human Sirt6 3-318 in complex with ADP-ribose · 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 6XV6 · PDBe 6XV6 · UniProt Q8N6T7
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