2VL8

CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF LETHAL TOXIN FROM CLOSTRIDIUM SORDELLII IN COMPLEX WITH UDP, CASTANOSPERMINE AND CALCIUM ION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Inhibition of the Glucosyltransferase Activity of Clostridial Rho/Ras-Glucosylating Toxins by Castanospermine.

Jank, T.Ziegler, M.O.P.Schulz, G.E.Aktories, K.

(2008) FEBS Lett 582: 2277

  • DOI: 10.1016/j.febslet.2008.05.025
  • Primary Citation of Related Structures:  
    2VL8

  • PubMed Abstract: 
  • Castanospermine was identified as an inhibitor of the Rho/Ras-glucosylating Clostridium sordellii lethal toxin and Clostridium difficile toxin B. Microinjection of castanospermine into embryonic bovine lung cells prevented the cytotoxic effects of toxins ...

    Castanospermine was identified as an inhibitor of the Rho/Ras-glucosylating Clostridium sordellii lethal toxin and Clostridium difficile toxin B. Microinjection of castanospermine into embryonic bovine lung cells prevented the cytotoxic effects of toxins. The crystal structure of the glucosyltransferase domain of C. sordellii lethal toxin in complex with castanospermine, UDP and a calcium ion was solved at a resolution of 2.3A. The inhibitor binds in a conformation that brings its four hydroxyl groups and its N-atom almost exactly in the positions of the four hydroxyls and of the ring oxygen of the glucosyl moiety of UDP-glucose, respectively.


    Organizational Affiliation

    Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Albert-Ludwigs-Universität, Albertstrasse 25, Freiburg, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOTOXIN LA, B, C546Paeniclostridium sordelliiMutation(s): 2 
Gene Names: tcsL
EC: 3.4.22 (UniProt), 2.4.1 (UniProt)
UniProt
Find proteins for Q46342 (Paeniclostridium sordellii)
Explore Q46342 
Go to UniProtKB:  Q46342
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46342
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
UDP PDBBind:  2VL8 IC50: 3.00e+4 (nM) from 1 assay(s)
CTS Binding MOAD:  2VL8 IC50: 3.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.689α = 90
b = 191.332β = 90
c = 205.384γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance