3VTS

Crystal structure of a three finger toxin from snake venom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.426 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification and structural characterization of a new three-finger toxin hemachatoxin from Hemachatus haemachatus venom.

Girish, V.M.Kumar, S.Joseph, L.Jobichen, C.Kini, R.M.Sivaraman, J.

(2012) Plos One 7: e48112-e48112

  • DOI: 10.1371/journal.pone.0048112

  • PubMed Abstract: 
  • Snake venoms are rich sources of biologically active proteins and polypeptides. Three-finger toxins are non-enzymatic proteins present in elapid (cobras, kraits, mambas and sea snakes) and colubrid venoms. These proteins contain four conserved disulf ...

    Snake venoms are rich sources of biologically active proteins and polypeptides. Three-finger toxins are non-enzymatic proteins present in elapid (cobras, kraits, mambas and sea snakes) and colubrid venoms. These proteins contain four conserved disulfide bonds in the core to maintain the three-finger folds. Although all three-finger toxins have similar fold, their biological activities are different. A new three-finger toxin (hemachatoxin) was isolated from Hemachatus haemachatus (Ringhals cobra) venom. Its amino acid sequence was elucidated, and crystal structure was determined at 2.43 Å resolution. The overall fold is similar to other three-finger toxins. The structure and sequence analysis revealed that the fold is maintained by four highly conserved disulfide bonds. It exhibited highest similarity to particularly P-type cardiotoxins that are known to associate and perturb the membrane surface with their lipid binding sites. Also, the increased B value of hemachotoxin loop II suggests that loop II is flexible and may remain flexible until its interaction with membrane phospholipids. Based on the analysis, we predict hemachatoxin to be cardiotoxic/cytotoxic and our future experiments will be directed to characterize the activity of hemachatoxin.


    Organizational Affiliation

    Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytotoxin 1
A, B
61Hemachatus haemachatusMutation(s): 0 
Find proteins for B3EWH9 (Hemachatus haemachatus)
Go to UniProtKB:  B3EWH9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.426 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.718α = 90.00
b = 50.057β = 90.00
c = 57.813γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2013-11-27
    Type: Database references