Caspase-3 E246A

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Thermodynamic, enzymatic and structural effects of removing a salt bridge at the base of loop 4 in (pro)caspase-3.

Walters, J.Swartz, P.Mattos, C.Clark, A.C.

(2011) Arch Biochem Biophys 508: 31-38

  • DOI: https://doi.org/10.1016/j.abb.2011.01.011
  • Primary Citation of Related Structures:  
    3PCX, 3PD0, 3PD1

  • PubMed Abstract: 

    Interactions between loops 2, 2' and 4, known as the loop bundle, stabilize the active site of caspase-3. Loop 4 (L4) is of particular interest due to its location between the active site and the dimer interface. We have disrupted a salt bridge between K242 and E246 at the base of L4 to determine its role in overall conformational stability and in maintaining the active site environment. Stability measurements show that only the K242A single mutant decreases stability of the dimer, whereas both single mutants and the double mutant demonstrate much lower activity compared to wild-type caspase-3. Structural studies of the caspase-3 variants show the involvement of K242 in hydrophobic interactions that stabilize helix 5, near the dimer interface, and the role of E246 appears to be to neutralize the positive charge of K242 within the hydrophobic cluster. Overall, the results suggest E246 and K242 are important in procaspase-3 for their interaction with neighboring residues, not with one another. Conversely, formation of the K242-E246 salt bridge in caspase-3 is needed for an accurate, stable conformation of loop L4 and proper active site formation in the mature enzyme.

  • Organizational Affiliation

    Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-3250Homo sapiensMutation(s): 1 
Gene Names: CASP3CPP32
UniProt & NIH Common Fund Data Resources
Find proteins for P42574 (Homo sapiens)
Explore P42574 
Go to UniProtKB:  P42574
GTEx:  ENSG00000164305 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42574
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CL

Download Ideal Coordinates CCD File 
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.176 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.613α = 90
b = 83.778β = 90
c = 96.228γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other