2F57

Crystal Structure Of The Human P21-Activated Kinase 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.185 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Crystal Structures of the p21-activated kinases PAK4, PAK5, and PAK6 reveal catalytic domain plasticity of active group II PAKs.

Eswaran, J.Lee, W.H.Debreczeni, J.E.Filippakopoulos, P.Turnbull, A.Fedorov, O.Deacon, S.W.Peterson, J.R.Knapp, S.

(2007) Structure 15: 201-213

  • DOI: https://doi.org/10.1016/j.str.2007.01.001
  • Primary Citation of Related Structures:  
    2BVA, 2C30, 2CDZ, 2F57

  • PubMed Abstract: 

    p21-activated kinases have been classified into two groups based on their domain architecture. Group II PAKs (PAK4-6) regulate a wide variety of cellular functions, and PAK deregulation has been linked to tumor development. Structural comparison of five high-resolution structures comprising all active, monophosphorylated group II catalytic domains revealed a surprising degree of domain plasticity, including a number of catalytically productive and nonproductive conformers. Rearrangements of helix alphaC, a key regulatory element of kinase function, resulted in an additional helical turn at the alphaC N terminus and a distortion of its C terminus, a movement hitherto unseen in protein kinases. The observed structural changes led to the formation of interactions between conserved residues that structurally link the glycine-rich loop, alphaC, and the activation segment and firmly anchor alphaC in an active conformation. Inhibitor screening identified six potent PAK inhibitors from which a tri-substituted purine inhibitor was cocrystallized with PAK4 and PAK5.


  • Organizational Affiliation

    University of Oxford, Structural Genomics Consortium, Botnar Research Centre, Oxford OX3 7LD, United Kingdom. jeyanthy.eswaran@sgc.ox.ac.uk


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 7
A, B
317Homo sapiensMutation(s): 1 
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P286 (Homo sapiens)
Explore Q9P286 
Go to UniProtKB:  Q9P286
PHAROS:  Q9P286
GTEx:  ENSG00000101349 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P286
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.185 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.661α = 90
b = 56.599β = 103.13
c = 120.764γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 23DClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Structure summary
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary