1YYN

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

• PDB DOI: https://doi.org/10.2210/pdb1YYN/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium tetani
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-02-25 Released: 2005-03-15 
• Deposition Author(s): Seetharaman, J., Eswaramoorthy, S., Kumaran, D., Swaminathan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.255 
• R-Value Observed: 0.255 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51.4 kDa 
• Atom Count: 3,814 
• Modelled Residue Count: 441 
• Deposited Residue Count: 441 
• Unique protein chains: 1

Macromolecules

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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-3)-alpha-D-galactopyranose-(1-4)-beta-D-glucopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan:  G74861PZ GlyCosmos:  G74861PZ GlyGen:  G74861PZ

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 70.907	α = 90
b = 78.93	β = 90
c = 90.977	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-15 
Deposition Author(s): Seetharaman, J., Eswaramoorthy, S., Kumaran, D., Swaminathan, S.

Revision History  

• 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