1IJL

Crystal structure of acidic phospholipase A2 from deinagkistrodon acutus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.,Sect.D 58: 104-110


  • 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 res ...

    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.


    Related Citations: 
    • Cloning and sequencing of gene encoding Phospholipase A2 from Agkistrodon Acutus
      Liu, X.L.,Pan, H.,Yang, G.Z.,Wu, X.F.,Zhou, Y.C.
      (1999) ACTA BIOCHIM.BIOPHYS.SINICA 31: 41


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
A, B
123Deinagkistrodon acutusEC: 3.1.1.4
Find proteins for Q7SID6 (Deinagkistrodon acutus)
Go to UniProtKB:  Q7SID6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.710α = 90.00
b = 38.000β = 99.35
c = 69.900γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance