› 6ljm

X-ray diffraction
1.78Å resolution

Crystal structure of human Sirt5 in complex with the fluorogenic tetrapeptide substrate P13

Released:
DOI: 10.2210/pdb6ljm/pdb
PDB entry 6ljm coloured by chain, front view.
PDB entry 6ljm coloured by chain, side view.
PDB entry 6ljm coloured by chain, top view.
Source organisms:
Primary publication:
Sensitive fluorogenic substrates for sirtuin deacylase inhibitor discovery.
Yang LL, Wang HL, Yan YH, Liu S, Yu ZJ, Huang MY, Luo Y, Zheng X, Yu Y, Li GB
Eur J Med Chem 192 112201 (2020)
PMID: 32163813

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-167022 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
NAD-dependent protein deacylase sirtuin-5, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 272 amino acids
Theoretical weight: 29.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NXA8 (Residues: 34-302; Coverage: 87%)
Gene names: SIR2L5, SIRT5
Sequence domains: Sir2 family
ACE-SER-LEU-GLY-SLL Chain: B
Molecule details ›
Chain: B
Length: 5 amino acids
Theoretical weight: 530 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand MCM 1 x MCM
1 modified residue:
Ligand SLL 1 x SLL

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Unit cell:
a: 42.2Å b: 55.275Å c: 124.524Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 0.165 0.197
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Lessons in Organic Fluorescent Probe Discovery.
Wagh et al. (2021)
5 more