Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 29.41 kDa 
• Atom Count: 2420 
• Modelled Residue Count: 255 
• Deposited Residue Count: 255 
• Unique protein chains: 3

2CNL

Crystal structures of caspase-3 in complex with aza-peptide epoxide inhibitors.

• DOI: 10.2210/pdb2CNL/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2006-05-22 Released: 2007-05-22 
• Deposition Author(s): Ganesan, R., Jelakovic, S., Campbell, A.J., Li, Z.Z., Asgian, J.L., Grutter, M.G., Powers, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.217 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Literature

Exploring the S4 and S1 Prime Subsite Specificities in Caspase-3 with Aza-Peptide Epoxide Inhibitors

Ganesan, R., Jelakovic, S., Campbell, A.J., Li, Z.Z., Asgian, J.L., Powers, J.C., Grutter, M.G.

(2006) Biochemistry 45: 9059

• PubMed: 16866351 
• DOI: 10.1021/bi060364p
• Primary Citation of Related Structures:  
  2CNO, 2CNN, 2CNL, 2CNK, 2CDR


• PubMed Abstract: 
  

Caspase-3 is a prototypic executioner caspase that plays a central role in apoptosis. Aza-peptide epoxides are a novel class of irreversible inhibitors that are highly specific for clan CD cysteine proteases. The five crystal structures of caspase-3-aza-peptide epoxide inhibitor complexes reported here reveal the structural basis for the mechanism of inhibition and the specificities at the S1' and the S4 subsites. Unlike the clan CA cysteine proteases, the catalytic histidine in caspase-3 plays a critical role during protonation and subsequent ring opening of the epoxide moiety and facilitates the nucleophilic attack by the active site cysteine. The nucleophilic attack takes place on the C3 carbon atom of the epoxide and results in an irreversible alkylation of the active site cysteine residue. A favorable network of hydrogen bonds involving the oxyanion hole, catalytic histidine, and the atoms in the prime site of the inhibitor enhance the binding affinity and specificity of the aza-peptide epoxide inhibitors toward caspase-3. The studies also reveal that subtle movements of the N-terminal loop of the beta-subunit occur when the P4 Asp is replaced by a P4 Ile, whereas the N-terminal loop and the safety catch Asp179 are completely disordered when the P4 Asp is replaced by P4 Cbz group.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CASPASE-3 SUBUNIT P17	A	147	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
CASPASE-3 SUBUNIT P12	B	103	Homo sapiens	Mutation(s): 0  Gene Names: CASP3, CPP32 EC: 3.4.22.56
Find proteins for P42574 (Homo sapiens) Explore P42574  Go to UniProtKB:  P42574
NIH Common Fund Data Resources
PHAROS:  P42574 GTEx:  ENSG00000164305

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
AZA-PEPTIDE EPOXIDE	I	5	synthetic construct	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000672	I	CBZ-ASP-GLU-VAL-azaASP-EP-CO-NH-CH2PH	Peptide-like /  Enzyme inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.217 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.694	α = 90
b = 83.963	β = 90
c = 96.271	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-22 
• Released Date: 2007-05-22 
Deposition Author(s): Ganesan, R., Jelakovic, S., Campbell, A.J., Li, Z.Z., Asgian, J.L., Grutter, M.G., Powers, J.C.

Revision History  

• Version 1.0: 2007-05-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2012-11-30
  Changes: Other
• Version 1.3: 2017-02-08
  Changes: Source and taxonomy, Structure summary
• Version 1.4: 2017-06-28
  Changes: Data collection