4K1E

Atomic resolution crystal structures of Kallikrein-Related Peptidase 4 complexed with a modified SFTI inhibitor FCQR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Direct and indirect mechanisms of KLK4 inhibition revealed by structure and dynamics

Riley, B.T.Ilyichova, O.Costa, M.G.S.Porebski, B.T.de Veer, S.J.Swedberg, J.E.Kass, I.Harris, J.M.Hoke, D.E.Buckle, A.M.

(2016) Sci Rep 6: 35385-35385

  • DOI: https://doi.org/10.1038/srep35385
  • Primary Citation of Related Structures:  
    4K1E, 4K8Y, 4KGA

  • PubMed Abstract: 

    The kallikrein-related peptidase (KLK) family of proteases is involved in many aspects of human health and disease. One member of this family, KLK4, has been implicated in cancer development and metastasis. Understanding mechanisms of inactivation are critical to developing selective KLK4 inhibitors. We have determined the X-ray crystal structures of KLK4 in complex with both sunflower trypsin inhibitor-1 (SFTI-1) and a rationally designed SFTI-1 derivative to atomic (~1 Å) resolution, as well as with bound nickel. These structures offer a structural rationalization for the potency and selectivity of these inhibitors, and together with MD simulation and computational analysis, reveal a dynamic pathway between the metal binding exosite and the active site, providing key details of a previously proposed allosteric mode of inhibition. Collectively, this work provides insight into both direct and indirect mechanisms of inhibition for KLK4 that have broad implications for the enzymology of the serine protease superfamily, and may potentially be exploited for the design of therapeutic inhibitors.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kallikrein-4223Homo sapiensMutation(s): 0 
Gene Names: KLK4
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5K2 (Homo sapiens)
Explore Q9Y5K2 
Go to UniProtKB:  Q9Y5K2
PHAROS:  Q9Y5K2
GTEx:  ENSG00000167749 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5K2
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Trypsin inhibitor 114Helianthus annuusMutation(s): 3 
UniProt
Find proteins for Q4GWU5 (Helianthus annuus)
Explore Q4GWU5 
Go to UniProtKB:  Q4GWU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4GWU5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
C [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
LI
Query on LI

Download Ideal Coordinates CCD File 
D [auth A]LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.78α = 90
b = 63.306β = 115.66
c = 41.181γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Other
  • Version 1.2: 2016-11-02
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description