We've built a new version of this page with an interactive 3D viewer. Try it out in beta and help us improve:

3dv0

X-ray diffraction
2.5Å resolution

Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex

Released:
Model geometry
Fit model/data

Function and Biology Details

Reactions catalysed:
[N(6)-[(R)-lipoyl]-L-lysyl-[protein] + pyruvate + H(+) = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CO2., N(6)-[(R)-lipoyl]-L-lysyl-[protein] + pyruvate + H(+) = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CO2., N(6)-[(R)-lipoyl]-L-lysyl-[protein] + pyruvate + H(+) = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CO2., N(6)-[(R)-lipoyl]-L-lysyl-[protein] + pyruvate + H(+) = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CO2., N(6)-[(R)-lipoyl]-L-lysyl-[protein] + pyruvate + H(+) = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CO2., N(6)-[(R)-lipoyl]-L-lysyl-[protein] + pyruvate + H(+) = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CO2., N(6)-[(R)-lipoyl]-L-lysyl-[protein] + pyruvate + H(+) = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CO2., N(6)-[(R)-lipoyl]-L-lysyl-[protein] + pyruvate + H(+) = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CO2.]
[N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + acetyl-CoA = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CoA., N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + acetyl-CoA = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CoA.]
Biochemical function:
Cellular component:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-146012 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Pyruvate dehydrogenase E1 component subunit alpha Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 369 amino acids
Theoretical weight: 41.52 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P21873 (Residues: 1-369; Coverage: 100%)
Gene name: pdhA
Sequence domains: Dehydrogenase E1 component
Structure domains: Rossmann fold
Pyruvate dehydrogenase E1 component subunit beta Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 325 amino acids
Theoretical weight: 35.5 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P21874 (Residues: 1-325; Coverage: 100%)
Gene name: pdhB
Sequence domains:
Structure domains:
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex Chains: I, J

Ligands and Environments


Cofactor: Ligand TPW 4 x TPW
3 bound ligands:
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21
Unit cell:
a: 68.312Å b: 232.82Å c: 92.004Å
α: 90° β: 91.83° γ: 90°
R-values:
R R work R free
0.176 0.173 0.241
Expression system: Escherichia coli