PDBe 5lvp

X-ray diffraction
2.5Å resolution

Human PDK1 Kinase Domain in Complex with an HM-Peptide Bound to the PIF-Pocket


Function and Biology Details

Reaction catalysed:
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
3-phosphoinositide-dependent protein kinase 1 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 311 amino acids
Theoretical weight: 35.39 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
  • Canonical: O15530 (Residues: 50-359; Coverage: 56%)
Gene names: PDK1, PDPK1
Sequence domains: Protein kinase domain
Structure domains:
hydrophobic-motif peptide of PKB/Akt Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 15 amino acids
Theoretical weight: 1.51 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P21
Unit cell:
a: 47.83Å b: 168.51Å c: 94.88Å
α: 90° β: 93.06° γ: 90°
R R work R free
0.176 0.174 0.226
Expression systems:
  • Spodoptera frugiperda
  • Not provided