MolNFT v1 · #139503 · protein
Crystal structure of SIRT5 complexed with a fluorogenic small-molecule substrate subka
5XHS · NAD-dependent protein deacylase sirtuin-5, mitochondrial: “Crystal structure of SIRT5 complexed with a fluorogenic small-molecule substrate subka”. X-ray diffraction, 4 ligands (PHQ, SLL, MCM), 2 pockets (best druggability 0.69).…
- PDB
- 5XHS
- Type
- protein
- Length
- 262 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacylase sirtuin-5, mitochondrial
- EC
- 3.5.1.-
- UniProt
- Q9NXA8
- Ligands
- PHQ, SLL, MCM, ZN
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacylase sirtuin-5, mitochondrial (EC 3.5.1.-) | protein | 262 | 37% helix, 19% strand | Q9NXA8 |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · chains A
- SLL · (2S)-2-azanyl-6-[(4-hydroxy-4-oxo-butanoyl)amino]hexanoic acid · ligand · chains A
- MCM · 7-amino-4-methyl-chromen-2-one · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.69 | 0.87 | 29 | SLL |
| 2 | 65 | 0.34 | 0.77 | 20 | empty |
Compared structures
- 5XHS · Crystal structure of SIRT5 complexed with a fluorogenic small-molecule substrate SuBKA · 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 A 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 5XHS · PDBe 5XHS · UniProt Q9NXA8
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