› 2f5z

X-ray diffraction
2.18Å resolution

Crystal Structure of Human Dihydrolipoamide Dehydrogenase (E3) Complexed to the E3-Binding Domain of Human E3-Binding Protein

Released:
DOI: 10.2210/pdb2f5z/pdb
PDB entry 2f5z coloured by chain, front view.
PDB entry 2f5z coloured by chain, side view.
PDB entry 2f5z coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insight into interactions between dihydrolipoamide dehydrogenase (E3) and E3 binding protein of human pyruvate dehydrogenase complex.
Brautigam CA, Wynn RM, Chuang JL, Machius M, Tomchick DR, Chuang DT
Structure 14 611-21 (2006)
PMID: 16442803

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:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126249 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Dihydrolipoyl dehydrogenase, mitochondrial Chains: A, B, C, D, E, F, G, H, I, J
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J
Length: 474 amino acids
Theoretical weight: 50.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09622 (Residues: 36-509; Coverage: 93%)
Gene names: DLD, GCSL, LAD, PHE3
Sequence domains:
Structure domains:
Pyruvate dehydrogenase protein X component, mitochondrial Chains: K, L, M, N, O
Molecule details ›
Chains: K, L, M, N, O
Length: 64 amino acids
Theoretical weight: 7.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O00330 (Residues: 173-230; Coverage: 12%)
Gene names: PDHX, PDX1
Sequence domains: e3 binding domain
Structure domains: E3-binding domain

Ligands and Environments


Cofactor: Ligand FAD 10 x FAD
1 bound ligand:
Ligand SO4 39 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 171.153Å b: 187.728Å c: 224.392Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.205 0.205 0.242
Expression systems:
  • Escherichia coli
  • Escherichia coli BL21

Quick links

Citations

14 review citations

The pyruvate dehydrogenase complexes: structure-based function and regulation.
Patel et al. (2014)
13 more

6 mentions without citation

Structural insight into interactions between dihydrolipoamide dehydrogenase (E3) and E3 binding protein of human pyruvate dehydrogenase complex.
Brautigam et al. (2006)
5 more