› 5lvm

X-ray diffraction
1.26Å resolution

Human PDK1 Kinase Domain in Complex with Adenine Bound to the ATP-Binding Site

Released:
DOI: 10.2210/pdb5lvm/pdb
PDB entry 5lvm coloured by chain, front view.
PDB entry 5lvm coloured by chain, side view.
PDB entry 5lvm 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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127511 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-phosphoinositide-dependent protein kinase 1 Chain: A
Molecule details ›
Chain: A
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:

Ligands and Environments

2 bound ligands:
Ligand ADE 1 x ADE
Ligand DTD 1 x DTD
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: C2
Unit cell:
a: 148.02Å b: 44.44Å c: 47.78Å
α: 90° β: 102.11° γ: 90°
R-values:
R R work R free
0.135 0.134 0.155
Expression system: Spodoptera frugiperda

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Citations

8 review citations

AGC kinases, mechanisms of regulation ‎and innovative drug development.
Leroux et al. (2018)
7 more