2P2C

Inhibition of caspase-2 by a designed ankyrin repeat protein (DARPin)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.262 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Inhibition of Caspase-2 by a Designed Ankyrin Repeat Protein: Specificity, Structure, and Inhibition Mechanism.

Schweizer, A.Roschitzki-Voser, H.Amstutz, P.Briand, C.Gulotti-Georgieva, M.Prenosil, E.Binz, H.K.Capitani, G.Baici, A.Pluckthun, A.Grutter, M.G.

(2007) Structure 15: 625-636

  • DOI: https://doi.org/10.1016/j.str.2007.03.014
  • Primary Citation of Related Structures:  
    2P2C

  • PubMed Abstract: 

    Specific and potent caspase inhibitors are indispensable for the dissection of the intricate pathways leading to apoptosis. We selected a designed ankyrin repeat protein (DARPin) from a combinatorial library that inhibits caspase-2 in vitro with a subnanomolar inhibition constant and, in contrast to the peptidic caspase inhibitors, with very high specificity for this particular caspase. The crystal structure of this inhibitor (AR_F8) in complex with caspase-2 reveals the molecular basis for the specificity and, together with kinetic analyses, the allosteric mechanism of inhibition. The structure also shows a conformation of the active site that can be exploited for the design of inhibitory compounds. AR_F8 is a specific inhibitor of an initiator caspase and has the potential to help identify the function of caspase-2 in the complex biological apoptotic signaling network.


  • Organizational Affiliation

    Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-2169Homo sapiensMutation(s): 1 
EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for P42575 (Homo sapiens)
Explore P42575 
Go to UniProtKB:  P42575
PHAROS:  P42575
GTEx:  ENSG00000106144 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42575
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-2106Homo sapiensMutation(s): 0 
Gene Names: CASP2
EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for P42575 (Homo sapiens)
Explore P42575 
Go to UniProtKB:  P42575
PHAROS:  P42575
GTEx:  ENSG00000106144 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42575
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-2169Homo sapiensMutation(s): 0 
Gene Names: CASP2
EC: 3.4.22
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.262 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.02α = 90
b = 229.21β = 90.11
c = 114.93γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Refinement description