Research workbench
Structure of human SIRT2 in complex with ADP-ribose
Analyse Structure of human SIRT2 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
- 3ZGV
- Type
- protein
- Length
- 596 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-2
- EC
- 3.5.1.-
- UniProt
- Q8IXJ6
- Ligands
- AR6, ZN
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 297 | 37% helix, 16% strand | Q8IXJ6 |
| B | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 299 | 38% helix, 17% strand | Q8IXJ6 |
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
- ZN · Zinc ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
- PGE · Triethylene glycol · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.79 | 0.84 | 62 | ACT, AR6 |
| 2 | 610 | 0.78 | 0.83 | 62 | ACT, AR6 |
| 3 | 573 | 0.65 | 0.76 | 77 | ACT, PGE |
| 4 | 516 | 0.62 | 0.75 | 44 | ACT, GOL |
| 5 | 136 | 0.42 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 996 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3ZGV · Structure of human SIRT2 in complex with ADP-ribose · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IXJ6 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-2 (Q8IXJ6) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q8IXJ6
- Elsewhere: RCSB PDB 3ZGV · PDBe 3ZGV · UniProt Q8IXJ6
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