1PSJ

ACIDIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of an acidic phospholipase A2 from the venom of Agkistrodon halys pallas at 2.0 A resolution.

Wang, X.Q.Yang, J.Gui, L.L.Lin, Z.J.Chen, Y.C.Zhou, Y.C.

(1996) J.Mol.Biol. 255: 669-676

  • DOI: 10.1006/jmbi.1996.0054

  • PubMed Abstract: 
  • The crystal structure of acidic phospholipase A2 from the venom of Agkistrodon halys pallas has been determined by molecular replacement at 2.0 A resolution to a crystallographic R-factor of 0.157. The overall structure of the molecule is very simila ...

    The crystal structure of acidic phospholipase A2 from the venom of Agkistrodon halys pallas has been determined by molecular replacement at 2.0 A resolution to a crystallographic R-factor of 0.157. The overall structure of the molecule is very similar to those of other phospholipase A2 species of known structure. The catalytic site, the hydrophobic channel and the N-terminal region show greatest structural conservation. The Ca(2+)-binding region has a conformation that resembles closely that of bovine PLA2 rather than Crotalus atrox PLA2. Compared with other PLA2 species, the conformation of the C-terminal ridge shows significant difference due to the insertion of two residues. A unique aromatic patch appears on one face of the molecules, surrounded by two acidic residues, the relevant features of this structure and their possible biological implications are discussed.


    Related Citations: 
    • Preliminary Crystallographic Study of the Platelet Aggregation Inhibitor from the Venom of Agkistrodon Halys Pallas
      Gui, L.,Niu, X.,Bi, R.,Lin, Z.,Chen, Y.
      (1992) Chin.Sci.Bull. 37: 1394


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Academia Sinica, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
A
124Gloydius halysEC: 3.1.1.4
Find proteins for P14418 (Gloydius halys)
Go to UniProtKB:  P14418
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.157 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 83.570α = 90.00
b = 83.570β = 90.00
c = 32.720γ = 120.00
Software Package:
Software NamePurpose
XENGENdata reduction
XENGENdata collection
X-PLORmodel building
X-PLORrefinement
XENGENdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1995-05-24 
  • Released Date: 1996-07-11 
  • Deposition Author(s): Wang, X.Q., Lin, Z.J.

Revision History 

  • Version 1.0: 1996-07-11
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance