Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.20 kDa 
• Atom Count: 4174 
• Modelled Residue Count: 476 
• Deposited Residue Count: 566 
• Unique protein chains: 2

1CP3

CRYSTAL STRUCTURE OF THE COMPLEX OF APOPAIN WITH THE TETRAPEPTIDE INHIBITOR ACE-DVAD-FMC

• DOI: 10.2210/pdb1CP3/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-12-12 Released: 1997-12-24 
• Deposition Author(s): Mittl, P.R.E., Dimarco, S., Gruetter, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.284 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Literature

Structure of recombinant human CPP32 in complex with the tetrapeptide acetyl-Asp-Val-Ala-Asp fluoromethyl ketone.

Mittl, P.R., Di Marco, S., Krebs, J.F., Bai, X., Karanewsky, D.S., Priestle, J.P., Tomaselli, K.J., Grutter, M.G.

(1997) J Biol Chem 272: 6539-6547

• PubMed: 9045680 
• DOI: 10.1074/jbc.272.10.6539
• Primary Citation of Related Structures:  
  1CP3


• PubMed Abstract: 
  

The cysteine protease CPP32 has been expressed in a soluble form in Escherichia coli and purified to >95% purity. The three-dimensional structure of human CPP32 in complex with the irreversible tetrapeptide inhibitor acetyl-Asp-Val-Ala-Asp fluoromethyl ketone was determined by x-ray crystallography at a resolution of 2.3 A. The asymmetric unit contains a (p17/p12)2 tetramer, in agreement with the tetrameric structure of the protein in solution as determined by dynamic light scattering and size exclusion chromatography. The overall topology of CPP32 is very similar to that of interleukin-1beta-converting enzyme (ICE); however, differences exist at the N terminus of the p17 subunit, where the first helix found in ICE is missing in CPP32. A deletion/insertion pattern is responsible for the striking differences observed in the loops around the active site. In addition, the P1 carbonyl of the ketone inhibitor is pointing into the oxyanion hole and forms a hydrogen bond with the peptidic nitrogen of Gly-122, resulting in a different state compared with the tetrahedral intermediate observed in the structure of ICE and CPP32 in complex with an aldehyde inhibitor. The topology of the interface formed by the two p17/p12 heterodimers of CPP32 is different from that of ICE. This results in different orientations of CPP32 heterodimers compared with ICE heterodimers, which could affect substrate recognition. This structural information will be invaluable for the design of small synthetic inhibitors of CPP32 as well as for the design of CPP32 mutants.

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Organizational Affiliation: 

Core Drug Discovery Technologies, Ciba-Geigy AG, CH-4002 Basel, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APOPAIN	A, C [auth B]	277	Homo sapiens	Mutation(s): 0  Gene Names: CASP3, CPP32 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 GTEx:  ENSG00000164305

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACETYL-ASP-VAL-ALA-ASP-FLUOROMETHYLKETONE	B [auth C], D	6	N/A	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000239	B [auth C], D	N-acetyl-L-alpha-aspartyl-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.284 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.9	α = 90
b = 69.1	β = 101.2
c = 93.8	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
MARXDS	data reduction
MARSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-12-12 
• Released Date: 1997-12-24 
Deposition Author(s): Mittl, P.R.E., Dimarco, S., Gruetter, M.G.

Revision History  

• Version 1.0: 1997-12-24
  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