Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.77 kDa 
• Atom Count: 1042 
• Residue Count: 120 
• Unique protein chains: 1

1OZ6

X-ray structure of acidic phospholipase A2 from Indian saw-scaled viper (Echis carinatus) with a potent platelet aggregation inhibitory activity

• DOI: 10.2210/pdb1OZ6/pdb

• Classification: HYDROLASE
• Organism(s): Echis carinatus
• Mutation(s): No 


• Deposited: 2003-04-08 Released: 2003-12-30 
• Deposition Author(s): Jasti, J., Paramasivam, M., Srinivasan, A., Singh, T.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.257 
• R-Value Work: 0.192 
• R-Value Observed: 0.207 

Literature

Structure of an acidic phospholipase A2 from Indian saw-scaled viper (Echis carinatus) at 2.6 A resolution reveals a novel intermolecular interaction.

Jasti, J., Paramasivam, M., Srinivasan, A., Singh, T.P.

(2004) Acta Crystallogr D Biol Crystallogr 60: 66-72

• PubMed: 14684894 
• DOI: 10.1107/s090744490302208x
• Primary Citation of Related Structures:  
  1OZ6


• PubMed Abstract: 
  

The crystal structure of an acidic phospholipase A(2) from the venom of Echis carinatus (saw-scaled viper; scPLA(2)) has been determined at 2.6 A resolution and refined to a crystallographic R factor of 0.192. Although the overall structure of scPLA(2) is essentially similar to those of other group II acidic PLA(2)s from different species, it shows unique features in several parts. Particularly noteworthy is the C-terminal part, which folds differently to those of other group II PLA(2)s. This part is considered to be responsible for inhibition of the platelet-aggregation activity. The calcium-binding loop is tightly organized with sevenfold coordination. Another striking feature of scPLA(2) is the involvement of Asn79 O(delta1) of a symmetry-related molecule in a coordination linkage with Ca(2+) of the calcium-binding loop. This is the first observation of an internal metal ion participating in an intermolecular interaction. The beta-wing of a molecule is deeply inserted into the hydrophobic channel of another molecule and forms several intermolecular interactions. This results in the formation of an infinite chain of molecules. These chains are stacked in an antiparallel arrangement in the crystals.

---

Organizational Affiliation: 

Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110 029, India.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phospholipase A2	A	120	Echis carinatus	Mutation(s): 0  EC: 3.1.1.4
Find proteins for Q7T3S7 (Echis carinatus) Explore Q7T3S7  Go to UniProtKB:  Q7T3S7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.257 
• R-Value Work: 0.192 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.963	α = 90
b = 57.876	β = 90
c = 33.682	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-08 
• Released Date: 2003-12-30 
Deposition Author(s): Jasti, J., Paramasivam, M., Srinivasan, A., Singh, T.P.

Revision History 

• Version 1.0: 2003-12-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance