1PAU

Crystal structure of the complex of apopain with the tetrapeptide aldehyde inhibitor AC-DEVD-CHO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The three-dimensional structure of apopain/CPP32, a key mediator of apoptosis.

Rotonda, J.Nicholson, D.W.Fazil, K.M.Gallant, M.Gareau, Y.Labelle, M.Peterson, E.P.Rasper, D.M.Ruel, R.Vaillancourt, J.P.Thornberry, N.A.Becker, J.W.

(1996) Nat Struct Biol 3: 619-625

  • DOI: 10.1038/nsb0796-619
  • Primary Citation of Related Structures:  
    1PAU

  • PubMed Abstract: 
  • Cysteine proteases related to mammalian interleukin-1 beta converting enzyme (ICE) and to its Caenorhabditis elegans homologue, CED-3, play a critical role in the biochemical events that culminate in apoptosis. We have determined the three-dimensiona ...

    Cysteine proteases related to mammalian interleukin-1 beta converting enzyme (ICE) and to its Caenorhabditis elegans homologue, CED-3, play a critical role in the biochemical events that culminate in apoptosis. We have determined the three-dimensional structure of a complex of the human CED-3 homologue CPP32/apopain with a potent tetrapeptide-aldehyde inhibitor. The protein resembles ICE in overall structure, but its S4 subsite is strikingly different in size and chemical composition. These differences account for the variation in specificity between the ICE- and CED-3-related proteases and enable the design of specific inhibitors that can probe the physiological functions of the proteins and disease states with which they are associated.


    Related Citations: 
    • Identification and Inhibition of the Ice/Ced-3 Protease Necessary for Mammalian Apoptosis
      Nicholson, D.W., Ali, A., Thornberry, N.A., Vaillancourt, J.P., Ding, C.K., Gallant, M., Gareau, Y., Griffin, P.R., Labelle, M., Lazebnik, Y.A., Munday, N.A., Raju, S.M., Smulson, M.E., Yamin, T.T., Yu, V.L., Miller, D.K.
      (1995) Nature 376: 37

    Organizational Affiliation

    Department of Biochemistry, Merck Research Laboratories, Rahway, New Jersey 07065-0900, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
APOPAINA147Homo sapiensMutation(s): 0 
Gene Names: CASP3CPP32
EC: 3.4.22 (PDB Primary Data), 3.4.22.56 (UniProt)
Find proteins for P42574 (Homo sapiens)
Explore P42574 
Go to UniProtKB:  P42574
NIH Common Fund Data Resources
PHAROS  P42574
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
APOPAINB102Homo sapiensMutation(s): 0 
Gene Names: CASP3CPP32
EC: 3.4.22 (PDB Primary Data), 3.4.22.56 (UniProt)
Find proteins for P42574 (Homo sapiens)
Explore P42574 
Go to UniProtKB:  P42574
NIH Common Fund Data Resources
PHAROS  P42574
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ACE-ASP-GLU-VAL-ASJC5N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000422
Query on PRD_000422
CAc-Asp-Glu-Val-Asp-AldehydePeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.81α = 90
b = 84.62β = 90
c = 96.79γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SAINTdata reduction
SAINTdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2017-11-29
    Changes: Derived calculations, Other