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 
  • R-Value Observed: 0.161 

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, 4A07

  • 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 atypical PKCζ and found that the inhibition by the N-terminal region cannot be explained by a simple pseudosubstrate inhibitory mechanism ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1A311Homo sapiensMutation(s): 2 
Gene Names: PDPK1PDK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O15530 (Homo sapiens)
Explore O15530 
Go to UniProtKB:  O15530
PHAROS:  O15530
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
AZ7
Query on AZ7

Download Ideal Coordinates CCD File 
C [auth A], D [auth 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

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.21α = 90
b = 44.03β = 101.23
c = 47.67γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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