1I1E | pdb_00001i1e

CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH DOXORUBICIN

• PDB DOI: https://doi.org/10.2210/pdb1I1E/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium botulinum
• Mutation(s): No 


• Deposited: 2001-02-01 Released: 2001-11-21 
• Deposition Author(s): Eswaramoorthy, S., Kumaran, D., Swaminathan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.276 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.221 (DCC) 

Starting Model: experimental

Literature

Crystallographic evidence for doxorubicin binding to the receptor-binding site in Clostridium botulinum neurotoxin B.

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

(2001) Acta Crystallogr D Biol Crystallogr 57: 1743-1746

• PubMed: 11679763 
• DOI: https://doi.org/10.1107/s0907444901013531
• Primary Citation Related Structures: 
  1I1E


• PubMed Abstract: 
  

  The neurotoxins of Clostridium botulinum and tetanus bind to gangliosides as a first step of their toxin activity. Identifying suitable receptors that compete with gangliosides could prevent toxin binding to the neuronal cells. A possible ganglioside-binding site of the botulinum neurotoxin B (BoNT/B) has already been proposed and evidence is now presented for a drug binding to botulinum neurotoxin B from structural studies. Doxorubicin, a well known DNA intercalator, binds to the neurotoxin at the receptor-binding site proposed earlier. The structure of the BoNT/B-doxorubicin complex reveals that doxorubicin has interactions with the neurotoxin similar to those of sialyllactose. The aglycone moiety of the doxorubicin stacks with tryptophan 1261 and interacts with histidine 1240 of the binding domain. Here, the possibility is presented of designing a potential antagonist for these neurotoxins from crystallographic analysis of the neurotoxin-doxorubicin complex, which will be an excellent lead compound.

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Organizational Affiliation: 
• Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 151.54 kDa 
• Atom Count: 11,016 
• Modeled Residue Count: 1,287 
• Deposited Residue Count: 1,290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BOTULINUM NEUROTOXIN TYPE B	A	1,290	Clostridium botulinum	Mutation(s): 0  EC: 3.4.24.69
UniProt
Find proteins for P10844 (Clostridium botulinum) Explore P10844  Go to UniProtKB:  P10844

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DM2	B [auth A]	DOXORUBICIN C27 H29 N O11 AOJJSUZBOXZQNB-TZSSRYMLSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.276 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.221 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.27	α = 90
b = 122.93	β = 112.95
c = 95.42	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-11-21 
Deposition Author(s): Eswaramoorthy, S., Kumaran, D., Swaminathan, S.

Revision History  

• Version 1.0: 2001-11-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary