› 2zdy

X-ray diffraction
2.4Å resolution

Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4

Released:
DOI: 10.2210/pdb2zdy/pdb
PDB entry 2zdy coloured by chain, front view.
PDB entry 2zdy coloured by chain, side view.
PDB entry 2zdy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4.
Kukimoto-Niino M, Tokmakov A, Terada T, Ohbayashi N, Fujimoto T, Gomi S, Shiromizu I, Kawamoto M, Matsusue T, Shirouzu M, Yokoyama S
Acta Crystallogr D Biol Crystallogr 67 763-73 (2011)
PMID: 21904029

Function and Biology Details

Reaction catalysed: 
ATP + [pyruvate dehydrogenase (acetyl-transferring)] = ADP + [pyruvate dehydrogenase (acetyl-transferring)] phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172541 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 394 amino acids
Theoretical weight: 44.77 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q16654 (Residues: 20-411; Coverage: 95%)
Gene names: PDHK4, PDK4
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand ADP 2 x ADP
Ligand EPE 1 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32B2
Spacegroup: P21
Unit cell:
a: 70.713Å b: 69.09Å c: 81.492Å
α: 90° β: 99.66° γ: 90°
R-values:
R R work R free
0.19 0.19 0.245
Expression system: Spodoptera frugiperda

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Citations

5 review citations

Anticancer agents that counteract tumor glycolysis.
Granchi et al. (2012)
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