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 PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 29.17 kDa 
• Atom Count: 2427 
• Modelled Residue Count: 254 
• Deposited Residue Count: 255 
• Unique protein chains: 3

2DKO

Extended substrate recognition in caspase-3 revealed by high resolution X-ray structure analysis

• DOI: 10.2210/pdb2DKO/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-04-12 Released: 2006-07-04 
• Deposition Author(s): Mittl, P.R.E., Ganesan, R., Jelakovic, S., Grutter, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 0.175 
• R-Value Work: 0.142 
• R-Value Observed: 0.142 

Literature

Extended Substrate Recognition in Caspase-3 Revealed by High Resolution X-ray Structure Analysis

Ganesan, R., Mittl, P.R.E., Jelakovic, S., Grutter, M.G.

(2006) J Mol Biol 359: 1378-1388

• PubMed: 16787777 
• DOI: 10.1016/j.jmb.2006.04.051
• Primary Citation of Related Structures:  
  2CJX, 2CJY, 2DKO


• PubMed Abstract: 
  

Caspases are cysteine proteases involved in the signalling cascades of programmed cell death in which caspase-3 plays a central role, since it propagates death signals from intrinsic and extrinsic stimuli to downstream targets. The atomic resolution (1.06 Angstroms) crystal structure of the caspase-3 DEVD-cmk complex reveals the structural basis for substrate selectivity in the S4 pocket. A low-barrier hydrogen bond is observed between the side-chains of the P4 inhibitor aspartic acid and Asp179 of the N-terminal tail of the symmetry related p12 subunit. Site-directed mutagenesis of Asp179 confirmed the significance of this residue in substrate recognition. In the 1.06 Angstroms crystal structure, a radiation damage induced rearrangement of the inhibitor methylketone moiety was observed. The carbon atom that in a substrate would represent the scissile peptide bond carbonyl carbon clearly shows a tetrahedral coordination and resembles the postulated tetrahedral intermediate of the acylation reaction.

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Organizational Affiliation: 

Biochemisches Institut, Universität Zürich, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-3	A	146	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	B	103	Homo sapiens	Mutation(s): 1  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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PHQ-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE	I	6	N/A	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000277	I	N-[(benzyloxy)carbonyl]-L-alpha-aspartyl-L-alpha-glutamyl-N-[(1S)-1-(carboxymethyl)-3-chloro-2-oxopropyl]-L-valinamide	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 0.175 
• R-Value Work: 0.142 
• R-Value Observed: 0.142 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.65	α = 90
b = 83.89	β = 90
c = 96.16	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
AMoRE	phasing
SHELXL-97	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-04-12 
• Released Date: 2006-07-04 
Deposition Author(s): Mittl, P.R.E., Ganesan, R., Jelakovic, S., Grutter, M.G.

Revision History  

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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: 2014-04-02
  Changes: Structure summary