Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 13.72 kDa 
• Atom Count: 987 
• Modelled Residue Count: 122 
• Deposited Residue Count: 122 
• Unique protein chains: 1

3VTS

Crystal structure of a three finger toxin from snake venom

• DOI: 10.2210/pdb3VTS/pdb

• Classification: TOXIN
• Organism(s): Hemachatus haemachatus
• Mutation(s): No 


• Deposited: 2012-06-06 Released: 2012-11-07 
• Deposition Author(s): Jobichen, C., Sivaraman, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.281 
• R-Value Work: 0.232 
• R-Value Observed: 0.237 

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

• PubMed: 23144733 
• DOI: 10.1371/journal.pone.0048112
• Primary Citation of Related Structures:  
  3VTS


• 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 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytotoxin 1	A, B	61	Hemachatus haemachatus	Mutation(s): 0
Find proteins for B3EWH9 (Hemachatus haemachatus) Explore B3EWH9  Go to UniProtKB:  B3EWH9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.281 
• R-Value Work: 0.232 
• R-Value Observed: 0.237 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.718	α = 90
b = 50.057	β = 90
c = 57.813	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-06 
• Released Date: 2012-11-07 
Deposition Author(s): Jobichen, C., Sivaraman, J.

Revision History  

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