2VU9

CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE A BINDING DOMAIN IN COMPLEX WITH GT1B

• PDB DOI: https://doi.org/10.2210/pdb2VU9/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium botulinum A
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-05-22 Released: 2008-08-26 
• Deposition Author(s): Stenmark, P., Dupuy, J., Stevens, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.186 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 53.03 kDa 
• Atom Count: 4,008 
• Modelled Residue Count: 425 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BOTULINUM NEUROTOXIN A HEAVY CHAIN	A	444	Clostridium botulinum A	Mutation(s): 0  EC: 3.4.24.69
UniProt
Find proteins for P0DPI1 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)) Explore P0DPI1  Go to UniProtKB:  P0DPI1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	B	6		N/A
Glycosylation Resources
GlyTouCan:  G46677TE GlyCosmos:  G46677TE GlyGen:  G46677TE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.186 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.7	α = 90
b = 116.11	β = 90
c = 105.52	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Stenmark, P., Dupuy, J., Stevens, R.C.

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary