2H4C

Structure of Daboiatoxin (heterodimeric PLA2 venom)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.220 
  • R-Value Observed: 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 D Biol Crystallogr 63: 722-729

  • DOI: 10.1107/S0907444907016204
  • Primary Citation of Related Structures:  
    2H4C

  • 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 the venom of D ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipase A2-IIIA, C, E, G122Daboia siamensisMutation(s): 0 
EC: 3.1.1.4
Membrane Entity: Yes 
UniProt
Find proteins for Q7T2R1 (Daboia siamensis)
Explore Q7T2R1 
Go to UniProtKB:  Q7T2R1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7T2R1
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipase A2-IIB, D, F, H122Daboia siamensisMutation(s): 0 
EC: 3.1.1.4
Membrane Entity: Yes 
UniProt
Find proteins for Q7T3T5 (Daboia siamensis)
Explore Q7T3T5 
Go to UniProtKB:  Q7T3T5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7T3T5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.977α = 90
b = 66.977β = 90
c = 240.273γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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