A common binding site for disialyllactose and a tri-peptide in the C-fragment of tetanus neurotoxin

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


Common binding site for disialyllactose and tri-peptide in C-fragment of tetanus neurotoxin

Jayaraman, S.Eswaramoorthy, S.Kumaran, D.Swaminathan, S.

(2005) Proteins 61: 288-295

  • DOI: https://doi.org/10.1002/prot.20595
  • Primary Citation of Related Structures:  
    1YXW, 1YYN

  • PubMed Abstract: 

    Clostridial neurotoxins are comprised of botulinum (BoNT) and tetanus (TeNT), which share significant structural and functional similarity. Crystal structures of the binding domain of TeNT complexed with disialyllactose (DiSia) and a tri-peptide Tyr-Glu-Trp (YEW) have been determined to 2.3 and 2.2 A, respectively. Both DiSia and YEW bind in a shallow cleft region on the surface of the molecule in the beta-trefoil domain, interacting with a set of common residues, Asp1147, Asp1214, Asn1216, and Arg1226. DiSia and YEW binding at the same site in tetanus toxin provides a putative site that could be occupied either by a ganglioside moiety or a peptide. Soaking experiments with a mixture of YEW and DiSia show that YEW competes with DiSia, suggesting that YEW can be used to block ganglioside binding. A comparison with the TeNT binding domain in complex with small molecules, BoNT/A and /B, provides insight into the different modes of ganglioside binding.

  • Organizational Affiliation

    Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tetanus toxin441Clostridium tetaniMutation(s): 0 
Find proteins for P04958 (Clostridium tetani (strain Massachusetts / E88))
Explore P04958 
Go to UniProtKB:  P04958
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04958
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-beta-D-glucopyranose
Glycosylation Resources
GlyTouCan:  G74861PZ
GlyCosmos:  G74861PZ
GlyGen:  G74861PZ
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.907α = 90
b = 78.93β = 90
c = 90.977γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-25
    Changes: Data collection, Database references, Refinement description, Structure summary