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: 1.3 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/srep35385
  • Primary Citation of Related Structures:  

  • 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 ar ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kallikrein-4
A
223Homo sapiensMutation(s): 0 
Gene Names: KLK4 (EMSP1, PRSS17, PSTS)
EC: 3.4.21.-
Find proteins for Q9Y5K2 (Homo sapiens)
Go to Gene View: KLK4
Go to UniProtKB:  Q9Y5K2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Trypsin inhibitor 1
B
14Helianthus annuusMutation(s): 3 
Gene Names: sfti1
Find proteins for Q4GWU5 (Helianthus annuus)
Go to UniProtKB:  Q4GWU5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LI
Query on LI

Download SDF File 
Download CCD File 
A
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000973
Query on PRD_000973
BTrypsin inhibitor 1Polypeptide / Trypsin inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.140 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.780α = 90.00
b = 63.306β = 115.66
c = 41.181γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction
ADSCdata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Other
  • Version 1.2: 2016-11-02
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description