2H4C

Structure of Daboiatoxin (heterodimeric PLA2 venom)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and pharmacological comparison of daboiatoxin from Daboia russelli siamensis with viperotoxin F and vipoxin from other vipers.

Gopalan, G.Thwin, M.M.Gopalakrishnakone, P.Swaminathan, K.

(2007) ACTA CRYSTALLOGR.,SECT.D 63: 722-729

  • DOI: 10.1107/S0907444907016204

  • PubMed Abstract: 
  • Russell's viper (Vipera russelli, also known as Daboia russelli) is one of the major causes of fatal snakebites. To date, five Daboia russelli subspecies have been recognized. Daboiatoxin (DbTx) is the main lethal phospholipase A(2) (PLA(2)) toxin in ...

    Russell's viper (Vipera russelli, also known as Daboia russelli) is one of the major causes of fatal snakebites. To date, five Daboia russelli subspecies have been recognized. Daboiatoxin (DbTx) is the main lethal phospholipase A(2) (PLA(2)) toxin in the venom of D. russelli siamensis (Myanmar viper) and has strong neurotoxic, myotoxic and cytotoxic activities. DbTx and its homologous neurotoxins viperotoxin F from D. russelli formosensis (Taiwan viper) and vipoxin from the Bulgarian sand viper V. ammodytes meridionalis consist of complexes between a nontoxic acidic PLA(2) protein and an enzymatically active basic PLA(2). DbTx and viperotoxin F are presynaptic toxins, while vipoxin is postsynaptic. The two chains of DbTx have been separated and their PLA(2) enzymatic activity has been measured using the secretory PLA(2) assay kit. The enzymatic activity of DbTx chain B is reduced by 30% of its original activity by chain A in a unimolar ratio, thus indicating that DbTx chain A acts as an inhibitor. The lethal activity of the two chains has also been studied in male albino mice and chain A is less lethal than chain B. The crystal structure of DbTx has also been determined and its structural details are compared with those of the two homologues. Furthermore, an attempt is made to correlate the sequence and structural determinants of these toxins with their enzymatic activities and their pharmacological effects.


    Organizational Affiliation

    Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phospholipase A2-III
A, C, E, G
122Daboia siamensisMutation(s): 0 
EC: 3.1.1.4
Find proteins for Q7T2R1 (Daboia siamensis)
Go to UniProtKB:  Q7T2R1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phospholipase A2-II
B, D, F, H
122Daboia siamensisMutation(s): 0 
EC: 3.1.1.4
Find proteins for Q7T3T5 (Daboia siamensis)
Go to UniProtKB:  Q7T3T5
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.220 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 66.977α = 90.00
b = 66.977β = 90.00
c = 240.273γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance