› 5nhg

X-ray diffraction
2.27Å resolution

Crystal structure of the human dihydrolipoamide dehydrogenase

Released:
DOI: 10.2210/pdb5nhg/pdb
PDB entry 5nhg coloured by chain, front view.
PDB entry 5nhg coloured by chain, side view.
PDB entry 5nhg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of the disease-causing D444V mutant and the relevant wild type human dihydrolipoamide dehydrogenase.
Szabo E, Mizsei R, Wilk P, Zambo Z, Torocsik B, Weiss MS, Adam-Vizi V, Ambrus A
Free Radic Biol Med 124 214-220 (2018)
PMID: 29908278

Function and Biology Details

Reaction catalysed: 
Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140717 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dihydrolipoyl dehydrogenase, mitochondrial Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 495 amino acids
Theoretical weight: 52.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P09622 (Residues: 36-509; Coverage: 93%)
Gene names: DLD, GCSL, LAD, PHE3
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand FAD 8 x FAD
2 bound ligands:
Ligand TRS 7 x TRS
Ligand BTB 1 x BTB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P1
Unit cell:
a: 60.06Å b: 113.54Å c: 136.88Å
α: 83.18° β: 84.75° γ: 81.09°
R-values:
R R work R free
0.181 0.18 0.21
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Hydrogen-Deuterium Exchange Mass Spectrometry: A Novel Structural Biology Approach to Structure, Dynamics and Interactions of Proteins and Their Complexes.
Ozohanics et al. (2020)
2 more

2 mentions without citation

An Updated View on the Molecular Pathomechanisms of Human Dihydrolipoamide Dehydrogenase Deficiency in Light of Novel Crystallographic Evidence.
Ambrus A. (2019)
1 more