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PDBsum entry 1oz7

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protein Protein-protein interface(s) links
Toxin PDB id
1oz7
Jmol
Contents
Protein chains
131 a.a. *
123 a.a. *
Waters ×142
* Residue conservation analysis
PDB id:
1oz7
Name: Toxin
Title: Crystal structure of echicetin from the venom of indian saw- scaled viper (echis carinatus) at 2.4 resolution
Structure: Echicetin a-chain. Chain: a. Synonym: echicetin alpha-subunit. Echicetin b-chain. Chain: b. Fragment: residues 1-123. Synonym: echicetin beta-subunit
Source: Echis carinatus. Saw-scaled viper. Organism_taxid: 40353. Secretion: venom. Secretion: venom
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.188     R-free:   0.244
Authors: J.Jasti,M.Paramasivam,A.Srinivasan,T.P.Singh
Key ref:
J.Jasti et al. (2004). Crystal structure of echicetin from Echis carinatus (Indian saw-scaled viper) at 2.4A resolution. J Mol Biol, 335, 167-176. PubMed id: 14659748 DOI: 10.1016/j.jmb.2003.10.048
Date:
08-Apr-03     Release date:   30-Dec-03    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q7T248  (ECHA_ECHCA) -  Snaclec echicetin subunit alpha (Fragment)
Seq:
Struc:
135 a.a.
131 a.a.
Protein chain
Pfam   ArchSchema ?
Q7T247  (ECHB_ECHCA) -  Snaclec echicetin subunit beta
Seq:
Struc:
146 a.a.
123 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biochemical function     carbohydrate binding     1 term  

 

 
DOI no: 10.1016/j.jmb.2003.10.048 J Mol Biol 335:167-176 (2004)
PubMed id: 14659748  
 
 
Crystal structure of echicetin from Echis carinatus (Indian saw-scaled viper) at 2.4A resolution.
J.Jasti, M.Paramasivam, A.Srinivasan, T.P.Singh.
 
  ABSTRACT  
 
Echicetin is a heterodimeric protein from the venom of the Indian saw-scaled viper, Echis carinatus. It binds to platelet glycoprotein Ib (GPIb) and thus inhibits platelet aggregation. It has two subunits, alpha and beta, consisting of 131 and 123 amino acid residues, respectively. The two chains are linked with a disulphide bond. The level of amino acid sequence homology between two subunits is 50%. The protein was purified from the venom of E.carinatus and crystallized using ammonium sulphate as a precipitant. The crystal structure has been determined at 2.4A resolution and refined to an R-factor of 0.187. Overall dimensions of the heterodimer are approximately 80Ax35Ax35A. The backbone folds of the two subunits are similar. The central portions of the polypeptide chains of alpha and beta-subunits move into each other to form a tight dimeric association. The remaining portions of the chains of both subunits fold in a manner similar to those observed in the carbohydrate-binding domains of C-type lectins. In echicetin, the Ca(2+)-binding sites are not present, despite being topologically equivalent to other similar Ca(2+)-binding proteins of the superfamily. The residues Ser41, Glu43 and Glu47 in the calcium-binding proteins of the related family are conserved but the residues Glu126/120 are replaced by lysine at the corresponding sites in the alpha and beta-subunits.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Overall structure of echicetin. The a-subunit is represented in green and the b-subunit in red. The two chains are interconnected by a disulphide-bond formed between Cys78(a) and Cys75(b). The Figure was produced using the programs RIBBONS[31.] and POVRAY (http://www.povray.org).
Figure 5.
Figure 5. Surface potential representations of echicetin as viewed along the interchain disulphide bond (a, b and c). The blue colour corresponds to the positive and the red to negative potentials. The upper and lower halves of the molecule correspond to the a and the b-subunits, respectively. The Figure was produced using the program GRASP.[34.]
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 335, 167-176) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21256857 Z.Chen, J.Wu, Y.Zhang, X.Yang, G.Yu, S.Zhu, W.Lee, Q.Lu, and Y.Zhang (2011).
A novel platelet glycoprotein Ib-binding protein with human platelet aggregation-inhibiting activity from Trimeresurus jerdonii venom.
  Toxicon, 57, 672-679.  
18597489 E.Hooley, E.Papagrigoriou, A.Navdaev, A.V.Pandey, J.M.Clemetson, K.J.Clemetson, and J.Emsley (2008).
The crystal structure of the platelet activator aggretin reveals a novel (alphabeta)2 dimeric structure.
  Biochemistry, 47, 7831-7837.
PDB code: 3bx4
16206329 A.Bazaa, N.Marrakchi, M.El Ayeb, L.Sanz, and J.J.Calvete (2005).
Snake venomics: comparative analysis of the venom proteomes of the Tunisian snakes Cerastes cerastes, Cerastes vipera and Macrovipera lebetina.
  Proteomics, 5, 4223-4235.  
  16508096 G.Xu, Q.Huang, M.Teng, P.Liu, Y.Dong, and L.Niu (2005).
Crystallization and preliminary X-ray crystallographic analysis of agkicetin-C from Deinagkistrodon acutus venom.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 75-78.  
15502319 G.Xu, M.Teng, L.Niu, P.Liu, Y.Dong, Q.Liu, Q.Huang, and Q.Hao (2004).
Purification, characterization, crystallization and preliminary X-ray crystallographic analysis of two novel C-type lectin-like proteins: Aall-A and Aall-B from Deinagkistrodon acutus venom.
  Acta Crystallogr D Biol Crystallogr, 60, 2035-2037.  
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