1B4W

BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS-IMPLICATIONS FOR ITS ASSOCIATION AND ANTICOAGULANT ACTIVITIES BY X-RAY CRYSTALLOGRAPHY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of basic phospholipase A2 from Agkistrodon halys Pallas: implications for its association, hemolytic and anticoagulant activities.

Zhao, K.Zhou, Y.Lin, Z.

(2000) Toxicon 38: 901-916


  • PubMed Abstract: 
  • The basic phospholipase A2 (PLA2) from the venom of Agkistrodon halys Pallas is a potent hemolytic toxin and anticoagulant. Crystal structure of the enzyme complexed with detergent n-octyl beta-D-glucopyranoside (beta-OG) in monoclinic crystal form h ...

    The basic phospholipase A2 (PLA2) from the venom of Agkistrodon halys Pallas is a potent hemolytic toxin and anticoagulant. Crystal structure of the enzyme complexed with detergent n-octyl beta-D-glucopyranoside (beta-OG) in monoclinic crystal form has been determined to 2.6 A resolution. Beta-OG molecules were found in the hydrophobic channels of the enzyme. SDS-PAGE and dynamic light scattering measurements showed that the enzyme had a strong tendency to dimerise in aqueous solution. In the crystal structure the enzyme molecules associate into a tetramer with pseudo 222 symmetry, and the interfacial recognition site linked dimers constituting the tetramer have intensive interface interactions, and may be stable in solution. The structure reveals a unique positively charged face at the C-terminal region and a characteristic non-cationic 'anticoagulant' region (53-77). The face is supposed to be the hemolytic site, and based on sequence and structure comparison residues Trp70 and Glu53 instead of the basic residues in 'anticoagulant' region might play an important role in the anticoagulant activity.


    Related Citations: 
    • Refined Structure of Basic Phospholipase A2 from the Venom of Agkistrodon Halys Pallas in Orthorhombic Crystal Form I at 0.25Nm Resolution (in: C)
      Zhao, K.H.,Song, S.Y.,Lin, Z.J.,Zhou, Y.C.
      (1999) SCI.CHINA, SER.C: LIFE SCI. 42: 80


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PHOSPHOLIPASE A2)
A, B, C, D
122Gloydius halysEC: 3.1.1.4
Find proteins for O42187 (Gloydius halys)
Go to UniProtKB:  O42187
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG

Download SDF File 
Download CCD File 
A, D
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.453α = 90.00
b = 54.294β = 111.76
c = 108.388γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1998-12-30 
  • Released Date: 2000-01-12 
  • Deposition Author(s): Zhao, K.H., Lin, Z.J.

Revision History 

  • Version 1.0: 2000-01-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance