› 5lvp

X-ray diffraction
2.5Å resolution

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

Released:
DOI: 10.2210/pdb5lvp/pdb
PDB entry 5lvp coloured by chain, front view.
PDB entry 5lvp coloured by chain, side view.
PDB entry 5lvp coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase.
Schulze JO, Saladino G, Busschots K, Neimanis S, Süß E, Odadzic D, Zeuzem S, Hindie V, Herbrand AK, Lisa MN, Alzari PM, Gervasio FL, Biondi RM
Cell Chem Biol 23 1193-1205 (2016)
PMID: 27693059

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127513 (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
UniProt:
  • 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:
Ligand ATP 4 x ATP
Ligand CL 2 x CL
1 modified residue:
Ligand SEP 8 x SEP

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-values:
R R work R free
0.176 0.174 0.226
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

8 review citations

ACE2, the Receptor that Enables Infection by SARS-CoV-2: Biochemistry, Structure, Allostery and Evaluation of the Potential Development of ACE2 Modulators.
Gross et al. (2020)
7 more

1 mention without citation

Molecular Insights into the Regulation of 3-Phosphoinositide-Dependent Protein Kinase 1: Modeling the Interaction between the Kinase and the Pleckstrin Homology Domains.
Garcia-Viloca et al. (2022)