4A07

Human PDK1 Kinase Domain in Complex with Allosteric Activator PS171 Bound to the PIF-Pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Allosteric Regulation of Protein Kinase Pkczeta by the N-Terminal C1 Domain and Small Compounds to the Pif-Pocket.

Lopez-Garcia, L.A.Schulze, J.O.Frohner, W.Zhang, H.Suss, E.Weber, N.Navratil, J.Amon, S.Hindie, V.Zeuzem, S.Jorgensen, T.J.Alzari, P.M.Neimanis, S.Engel, M.Biondi, R.M.

(2011) Chem.Biol. 18: 1463

  • DOI: 10.1016/j.chembiol.2011.08.010
  • Primary Citation of Related Structures:  4A06

  • PubMed Abstract: 
  • Protein kinases are key mediators of cellular signaling, and therefore, their activities are tightly controlled. AGC kinases are regulated by phosphorylation and by N- and C-terminal regions. Here, we studied the molecular mechanism of inhibition of ...

    Protein kinases are key mediators of cellular signaling, and therefore, their activities are tightly controlled. AGC kinases are regulated by phosphorylation and by N- and C-terminal regions. Here, we studied the molecular mechanism of inhibition of atypical PKCζ and found that the inhibition by the N-terminal region cannot be explained by a simple pseudosubstrate inhibitory mechanism. Notably, we found that the C1 domain allosterically inhibits PKCζ activity and verified an allosteric communication between the PIF-pocket of atypical PKCs and the binding site of the C1 domain. Finally, we developed low-molecular-weight compounds that bind to the PIF-pocket and allosterically inhibit PKCζ activity. This work establishes a central role for the PIF-pocket on the regulation of PKCζ and allows us to envisage development of drugs targeting the PIF-pocket that can either activate or inhibit AGC kinases.


    Organizational Affiliation

    Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, 60590 Frankfurt, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1
A
311Homo sapiensGene Names: PDPK1 (PDK1)
EC: 2.7.11.1
Find proteins for O15530 (Homo sapiens)
Go to Gene View: PDPK1
Go to UniProtKB:  O15530
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
AZ7
Query on AZ7

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Download CCD File 
A
(3S)-3-(4-CHLOROPHENYL)-4-(5,7-DICHLORO-1H-BENZIMIDAZOL-2-YL)BUTANOIC ACID
C17 H13 Cl3 N2 O2
WMLLAHSMFYNLLO-JTQLQIEISA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
CSS
Query on CSS
A
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 148.210α = 90.00
b = 44.030β = 101.23
c = 47.670γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2011-12-21
    Type: Other