MolNFT v1 · #119523 · protein
SIRT2 in complex with a 13-mer trifluoroacetylated ran peptide
5FYQ · NAD-dependent protein deacetylase sirtuin-2: “SIRT2 in complex with a 13-mer trifluoroacetylated ran peptide”. X-ray diffraction, 2 ligands (ZN, SO4), 7 pockets (best druggability 0.74). MolNFT v1 #119523 on GenesisL1: 3D structure…
- PDB
- 5FYQ
- Type
- protein
- Length
- 563 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-2; Ran aa 31-43
- EC
- 3.5.1.-
- UniProt
- Q8IXJ6, P62826
- Ligands
- ZN, SO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 282 | 37% helix, 18% strand | Q8IXJ6 |
| B | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 266 | 36% helix, 18% strand | Q8IXJ6 |
| C | Ran aa 31-43 | protein | 7 | 0% helix, 43% strand | P62826 |
| D | Ran aa 31-43 | protein | 8 | 0% helix, 38% strand | P62826 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.74 | 0.88 | 32 | empty |
| 2 | 362 | 0.59 | 0.76 | 30 | empty |
| 3 | 215 | 0.53 | 0.77 | 34 | empty |
| 4 | 68 | 0.50 | 0.85 | 20 | SO4 |
| 5 | 178 | 0.49 | 0.77 | 29 | SO4 |
Interfaces
3 interfaces between chains.
- A–D · 633 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 617 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 545 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 disulfide (nonstandard, disulfide).
Compared structures
- 5FYQ · Sirt2 in complex with a 13-mer trifluoroacetylated Ran peptide · 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 Q8IXJ6
- Every structure of UniProt P62826
- Elsewhere: RCSB PDB 5FYQ · PDBe 5FYQ · UniProt Q8IXJ6 · UniProt P62826
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