Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51009.46 
• Atom Count: 3600 
• Residue Count: 441 
• Unique protein chains: 1

1YXW

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

• DOI: 10.2210/pdb1YXW/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium tetani (strain Massachusetts / E88)


• Deposited: 2005-02-22 Released: 2005-03-15 
• Deposition Author(s): Jayaraman, S., Eswaramoorthy, S., Kumaran, D., Swaminathan, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.274 
• R-Value Work: 0.224 

Literature

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

• PubMed: 16104015 
• DOI: 10.1002/prot.20595
• Primary Citation of Related Structures:  
  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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Tetanus toxin (Tentoxylysin)	A	441	Clostridium tetani (strain Massachusetts / E88)	Mutation(s): 0  Gene Names: tetX EC: 3.4.24.68
Find proteins for P04958 (Clostridium tetani (strain Massachusetts / E88)) Go to UniProtKB:  P04958

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
TYR	A	TYROSINE C9 H11 N O3 OUYCCCASQSFEME-QMMMGPOBSA-N
GLU	A	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
TRP	A	TRYPTOPHAN C11 H12 N2 O2 QIVBCDIJIAJPQS-VIFPVBQESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.274 
• R-Value Work: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 66.757	α = 90.00
b = 79.183	β = 90.00
c = 90.265	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
CNS	refinement
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-02-22 
• Released Date: 2005-03-15 
• Deposition Author(s): Jayaraman, S., Eswaramoorthy, S., Kumaran, D., Swaminathan, S.

Revision History 

• Version 1.0: 2005-03-15
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance