2QLF

Crystal Structure of Caspase-7 with inhibitor AC-DNLD-CHO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Plasticity of S2-S4 specificity pockets of executioner caspase-7 revealed by structural and kinetic analysis.

Agniswamy, J.Fang, B.Weber, I.T.

(2007) Febs J. 274: 4752-4765

  • DOI: 10.1111/j.1742-4658.2007.05994.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Many protein substrates of caspases are cleaved at noncanonical sites in comparison to the recognition motifs reported for the three caspase subgroups. To provide insight into the specificity and aid in the design of drugs to control cell death, crys ...

    Many protein substrates of caspases are cleaved at noncanonical sites in comparison to the recognition motifs reported for the three caspase subgroups. To provide insight into the specificity and aid in the design of drugs to control cell death, crystal structures of caspase-7 were determined in complexes with six peptide analogs (Ac-DMQD-Cho, Ac-DQMD-Cho, Ac-DNLD-Cho, Ac-IEPD-Cho, Ac-ESMD-Cho, Ac-WEHD-Cho) that span the major recognition motifs of the three subgroups. The crystal structures show that the S2 pocket of caspase-7 can accommodate diverse residues. Glu is not required at the P3 position because Ac-DMQD-Cho, Ac-DQMD-Cho and Ac-DNLD-Cho with varied P3 residues are almost as potent as the canonical Ac-DEVD-Cho. P4 Asp was present in the better inhibitors of caspase-7. However, the S4 pocket of executioner caspase-7 has alternate regions for binding of small branched aliphatic or polar residues similar to those of initiator caspase-8. The observed plasticity of the caspase subsites agrees very well with the reported cleavage of many proteins at noncanonical sites. The results imply that factors other than the P4-P1 sequence, such as exosites, contribute to the in vivo substrate specificity of caspases. The novel peptide binding site identified on the molecular surface of the current structures is suggested to be an exosite of caspase-7. These results should be considered in the design of selective small molecule inhibitors of this pharmacologically important protease.


    Organizational Affiliation

    Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30302, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-7
A, C
173Homo sapiensMutation(s): 0 
Gene Names: CASP7 (MCH3)
EC: 3.4.22.60
Find proteins for P55210 (Homo sapiens)
Go to Gene View: CASP7
Go to UniProtKB:  P55210
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Caspase-7
B, D
97Homo sapiensMutation(s): 0 
Gene Names: CASP7 (MCH3)
EC: 3.4.22.60
Find proteins for P55210 (Homo sapiens)
Go to Gene View: CASP7
Go to UniProtKB:  P55210
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Inhibitor AC-DNLD-CHO
E, F
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Peptide QGHGE
G
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000282
Query on PRD_000282
E,FN-acetyl-L-alpha-aspartyl-L-asparaginyl-N-[(1R)-2-carboxy-1-formylethyl]-L-leucinamidePeptide-like / Inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.464α = 90.00
b = 87.464β = 90.00
c = 185.825γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-12-12
    Type: Other