1I1E

CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH DOXORUBICIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1107/s0907444901013531
  • Primary Citation of 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 ...

    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.


    Related Citations: 
    • Structural Analysis of the Catalytic and Binding Sites of Clostridium botulinum Neurotoxin B
      Swaminathan, S., Eswaramoorthy, S.
      (2000) Nat Struct Biol 7: 693
    • Crystallization and Preliminary X-ray Analysis of Clostridium botulinum Neurotoxin Type B
      Swaminathan, S., Eswaramoorthy, S.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 1024

    Organizational Affiliation

    Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BOTULINUM NEUROTOXIN TYPE BA1290Clostridium botulinumMutation(s): 0 
Gene Names: botB
EC: 3.4.24.69
Find proteins for P10844 (Clostridium botulinum)
Explore P10844 
Go to UniProtKB:  P10844
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DM2
Query on DM2

Download Ideal Coordinates CCD File 
B [auth A]DOXORUBICIN
C27 H29 N O11
AOJJSUZBOXZQNB-TZSSRYMLSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DM2Kd:  9400   nM  Binding MOAD
DM2Kd :  9400   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.27α = 90
b = 122.93β = 112.95
c = 95.42γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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