4A06 | pdb_00004a06

Human PDK1 Kinase Domain in Complex with Allosteric Activator PS114 Bound to the PIF-Pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.198 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4A06

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.chembiol.2011.08.010
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 36.61 kDa 
  • Atom Count: 2,414 
  • Modeled Residue Count: 285 
  • Deposited Residue Count: 311 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1311Homo sapiensMutation(s): 2 
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
GTEx:  ENSG00000140992 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15530
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / 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
A06

Query on A06



Download:Ideal Coordinates CCD File
C [auth A](3S)-4-(5-chloro-1H-benzimidazol-2-yl)-3-(4-chlorophenyl)butanoic acid
C17 H14 Cl2 N2 O2
MOXSMEYUODNXTB-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
D [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.198 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.39α = 90
b = 44.1β = 100.07
c = 47.3γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary