Research workbench
Re-refined structure of the human SIRT2 apoform
Analyse Re-refined structure of the human SIRT2 apoform in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZGO
- Type
- protein
- Length
- 939 residues
- Chains
- 3
- 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
- ZN
- Pockets
- 15 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 318 | 43% helix, 15% strand | Q8IXJ6 |
| C | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 303 | 41% helix, 16% strand | Q8IXJ6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 7 copies · chains A, B, C
- P6G · Hexaethylene glycol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
- EOH · Ethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.62 | 0.77 | 56 | PGE |
| 2 | 435 | 0.61 | 0.76 | 59 | EDO |
| 3 | 459 | 0.60 | 0.74 | 51 | PGE |
| 4 | 246 | 0.52 | 0.76 | 36 | empty |
| 5 | 162 | 0.49 | 0.77 | 26 | empty |
Interfaces
2 interfaces between chains.
- A–B · 306 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 280 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3ZGO · Re-refined structure of the human Sirt2 apoform · 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 C against A, TM-score 0.90
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 3ZGO · PDBe 3ZGO · UniProt Q8IXJ6
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