2HBY

Crystal structure of human caspase-1 (Glu390->Ala) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Common Allosteric Site and Mechanism in Caspases

Scheer, J.M.Romanowski, M.J.Wells, J.A.

(2006) Proc.Natl.Acad.Sci.USA 103: 7595

  • DOI: 10.1073/pnas.0602571103
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We present a common allosteric mechanism for control of inflammatory and apoptotic caspases. Highly specific thiol-containing inhibitors of the human inflammatory caspase-1 were identified by using disulfide trapping, a method for site-directed small ...

    We present a common allosteric mechanism for control of inflammatory and apoptotic caspases. Highly specific thiol-containing inhibitors of the human inflammatory caspase-1 were identified by using disulfide trapping, a method for site-directed small-molecule discovery. These compounds became trapped by forming a disulfide bond with a cysteine residue in the cavity at the dimer interface approximately 15 A away from the active site. Mutational and structural analysis uncovered a linear circuit of functional residues that runs from one active site through the allosteric cavity and into the second active site. Kinetic analysis revealed robust positive cooperativity not seen in other endopeptidases. Recently, disulfide trapping identified a similar small-molecule site and allosteric transition in the apoptotic caspase-7 that shares only a 23% sequence identity with caspase-1. Together, these studies show a general small-molecule-binding site for functionally reversing the zymogen activation of caspases and suggest a common regulatory site for the allosteric control of inflammation and apoptosis.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, 1700 4th Street, San Francisco, CA 94143, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-1
A
178Homo sapiensMutation(s): 0 
Gene Names: CASP1 (IL1BC, IL1BCE)
EC: 3.4.22.36
Find proteins for P29466 (Homo sapiens)
Go to Gene View: CASP1
Go to UniProtKB:  P29466
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Caspase-1
B
88Homo sapiensMutation(s): 1 
Gene Names: CASP1 (IL1BC, IL1BCE)
EC: 3.4.22.36
Find proteins for P29466 (Homo sapiens)
Go to Gene View: CASP1
Go to UniProtKB:  P29466
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide
C
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_000338
Query on PRD_000338
CN-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamidePeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.227 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.270α = 90.00
b = 63.270β = 90.00
c = 160.933γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
CrystalCleardata collection
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other