1F1J | pdb_00001f1j

CRYSTAL STRUCTURE OF CASPASE-7 IN COMPLEX WITH ACETYL-ASP-GLU-VAL-ASP-CHO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.263 (Depositor) 
  • R-Value Work: 
    0.185 (Depositor) 
  • R-Value Observed: 
    0.185 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1F1J

This is version 1.5 of the entry. See complete history

Literature

The structures of caspases-1, -3, -7 and -8 reveal the basis for substrate and inhibitor selectivity.

Wei, Y.Fox, T.Chambers, S.P.Sintchak, J.Coll, J.T.Golec, J.M.Swenson, L.Wilson, K.P.Charifson, P.S.

(2000) Chem Biol 7: 423-432

  • DOI: https://doi.org/10.1016/s1074-5521(00)00123-x
  • Primary Citation Related Structures: 
    1F1J

  • PubMed Abstract: 

    Peptide inhibitors of caspases have helped define the role of these cysteine proteases in biology. Structural and biochemical characterization of the caspase enzymes may contribute to the development of new drugs for the treatment of caspase-mediated inflammation and apoptosis. The crystal structure of the previously unpublished caspase-7 (Csp7; 2.35 A) bound to the reversible tetrapeptide aldehyde inhibitor acetyl-Asp-Glu-Val-Asp-CHO is compared with crystal structures of caspases-1 (2.3 A), -3 (2.2 A), and -8 (2.65 A) bound to the same inhibitor. Csp7 is a close homolog of caspase-3 (Csp3), and these two caspases possess some quarternary structural characteristics that support their unique role among the caspase family. However, although Csp3 and Csp7 are quite similar overall, they were found to have a significantly different substitution pattern of amino acids in and around the S4-binding site. These structures span all three caspase subgroups, and provide a basis for inferring substrate and inhibitor binding, as well as selectivity for the entire caspase family. This information will influence the design of selective caspase inhibitors to further elucidate the role of caspases in biology and hopefully lead to the design of therapeutic agents to treat caspase-mediated diseases, such as rheumatoid arthritis, certain neurogenerative diseases and stroke.


  • Organizational Affiliation
    • Vertex Pharmaceuticals, Cambridge, MA 02139-4242, USA.

Macromolecule Content 

  • Total Structure Weight: 70.27 kDa 
  • Atom Count: 4,164 
  • Modeled Residue Count: 471 
  • Deposited Residue Count: 620 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CASPASE-7 PROTEASE
A, B
305Homo sapiensMutation(s): 0 
EC: 3.4.22 (PDB Primary Data), 3.4.22.60 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P55210 (Homo sapiens)
Explore P55210 
Go to UniProtKB:  P55210
PHAROS:  P55210
GTEx:  ENSG00000165806 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55210
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ACE-ASP-GLU-VAL-ASP-CHO
C, D
5N/AMutation(s): 0 

Small Molecules

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.263 (Depositor) 
  • R-Value Work:  0.185 (Depositor) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.18α = 90
b = 88.18β = 90
c = 186.23γ = 120
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    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: 2013-07-03
    Changes: Structure summary
  • Version 1.5: 2025-03-26
    Changes: Data collection, Database references, Derived calculations, Structure summary