Research workbench
Crystal structure of human SIRT5 in complex with fluor-de-lys peptide and resveratrol
Analyse Crystal structure of human SIRT5 in complex with fluor-de-lys peptide and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HDA
- Type
- protein
- Length
- 540 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase sirtuin-5, mitochondrial; Fluor-de-lys peptide
- EC
- 3.5.1.-
- UniProt
- Q9NXA8
- Ligands
- STL, ZN
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 267 | 33% helix, 18% strand | Q9NXA8 |
| B | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 270 | 29% helix, 19% strand | Q9NXA8 |
| F | Fluor-de-lys peptide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.76 | 0.86 | 53 | empty |
| 2 | 332 | 0.62 | 0.79 | 44 | STL |
| 3 | 113 | 0.45 | 0.79 | 25 | empty |
| 4 | 88 | 0.41 | 0.78 | 19 | empty |
| 5 | 62 | 0.31 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 975 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 527 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 252 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 4HDA · Crystal structure of human Sirt5 in complex with Fluor-de-Lys peptide and resveratrol · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NXA8 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacylase sirtuin-5… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9NXA8
- Elsewhere: RCSB PDB 4HDA · PDBe 4HDA · UniProt Q9NXA8
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