3QNW

Caspase-6 in complex with Z-VAD-FMK inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of human caspase-6 in complex with Z-VAD-FMK: New peptide binding mode observed for the non-canonical caspase conformation.

Muller, I.Lamers, M.B.Ritchie, A.J.Dominguez, C.Munoz-Sanjuan, I.Kiselyov, A.

(2011) Bioorg.Med.Chem.Lett. 21: 5244-5247

  • DOI: 10.1016/j.bmcl.2011.07.041

  • PubMed Abstract: 
  • Caspase-6 is a cysteine protease implicated in neuronal survival and apoptosis. Deregulation of caspase-6 activity was linked to several neurodegenerative disorders including Alzheimer's and Huntington's Diseases. Several recent studies on the struct ...

    Caspase-6 is a cysteine protease implicated in neuronal survival and apoptosis. Deregulation of caspase-6 activity was linked to several neurodegenerative disorders including Alzheimer's and Huntington's Diseases. Several recent studies on the structure of caspase-6 feature the caspase-6 zymogen, mature apo-caspase-6 as well as the Ac-VEID-CHO peptide complex. All structures share the same typical dimeric caspase conformation. However, mature apo-caspase-6 crystallized at low pH revealed a novel, non-canonical inactive caspase conformation speculated to represent a latent state of the enzyme suitable for the design of allosteric inhibitors. In this treatise we present the structure of caspase-6 in the non-canonical inactive enzyme conformation bound to the irreversible inhibitor Z-VAD-FMK. The complex features a unique peptide binding mode not observed previously.


    Organizational Affiliation

    BioFocus, Chesterford Research Park, Saffron Walden, Essex, CB10 1XL, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-6
A, C, E, G
156Homo sapiensMutation(s): 0 
Gene Names: CASP6 (MCH2)
EC: 3.4.22.59
Find proteins for P55212 (Homo sapiens)
Go to Gene View: CASP6
Go to UniProtKB:  P55212
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Caspase-6
B, D, F, H
100Homo sapiensMutation(s): 0 
Gene Names: CASP6 (MCH2)
EC: 3.4.22.59
Find proteins for P55212 (Homo sapiens)
Go to Gene View: CASP6
Go to UniProtKB:  P55212
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Z-VAD-FMK
X, Y, Z
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000338
Query on PRD_000338
X,Y,ZN-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamidePeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 87.206α = 90.00
b = 65.446β = 91.24
c = 91.718γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
GDAdata collection
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2013-02-27
    Type: Other