1IJL

Crystal structure of acidic phospholipase A2 from deinagkistrodon acutus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 

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This is version 1.3 of the entry. See complete history


Literature

Structure of an acidic phospholipase A2 from the venom of Deinagkistrodon acutus.

Gu, L.Zhang, H.Song, S.Zhou, Y.Lin, Z.

(2002) Acta Crystallogr D Biol Crystallogr 58: 104-110

  • DOI: https://doi.org/10.1107/s0907444901018170
  • Primary Citation of Related Structures:  
    1IJL

  • PubMed Abstract: 

    An acidic phospholipase A(2) was purified from Deinagkistrodon acutus (Agkistrodon acutus) which displays an inhibitory effect on platelet aggregation. The three-dimensional structure of the enzyme was determined by molecular replacement at 2.6 A resolution with a crystallographic R factor of 18.40% (R(free) = 22.50%) and reasonable stereochemistry. Two molecules in the asymmetric unit form a dimer and the dimer formation accompanies a significant conformational adaptation of segment 14-23, a constituent of the 'interface recognition site' (IRS). This probably reflects the inherent structural flexibility of the IRS. The possible expansion of the site for inhibiting platelet aggregation as proposed previously [Wang et al. (1996), J. Mol. Biol. 255, 669-676] is discussed.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHOLIPASE A2
A, B
123Deinagkistrodon acutusMutation(s): 0 
EC: 3.1.1.4
UniProt
Find proteins for Q7SID6 (Deinagkistrodon acutus)
Explore Q7SID6 
Go to UniProtKB:  Q7SID6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SID6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.71α = 90
b = 38β = 99.35
c = 69.9γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description