1A2A

AGKISTROTOXIN, A PHOSPHOLIPASE A2-TYPE PRESYNAPTIC NEUROTOXIN FROM AGKISTRODON HALYS PALLAS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of agkistrodotoxin, a phospholipase A2-type presynaptic neurotoxin from agkistrodon halys pallas.

Tang, L.Zhou, Y.C.Lin, Z.J.

(1998) J.Mol.Biol. 282: 1-11

  • DOI: 10.1006/jmbi.1998.1987

  • PubMed Abstract: 
  • The crystal structure of agkistrodotoxin containing eight copies of molecules in the asymmetric unit has been determined at 2.8 A resolution to a crystallographic R factor of 0.207 by the molecular replacement technique. Two spatially adjacent region ...

    The crystal structure of agkistrodotoxin containing eight copies of molecules in the asymmetric unit has been determined at 2.8 A resolution to a crystallographic R factor of 0.207 by the molecular replacement technique. Two spatially adjacent regions of agkistrodotoxin molecule, turn 55-61 and stretch 85-91, are remarkably different from those of non-neurotoxic isoforms in conformation and electrostatic characteristics. These regions are likely to be involved in the recognition of agkistrodotoxin towards the specific receptor at the presynaptic membrane. The structural comparison of the interfacial recognition site with non-neurotoxic isoforms reveals a decreased hydrophobicity and lack of residues with bulky hydrophobic side-chains (i.e. Trp) to serve as membrane anchors. This structural feature of agkistrodotoxin may be related to the reduced non-specific binding of the toxin to non-targeted membrane before it arrives at the presynaptic membrane and recognizes the putative receptor. A unique hydrophobic patch including residues I19, P20, F21, A23, F24, M118 and F119 is found on the surface of the molecule near the entrance of the hydrophobic channel which plays an important role in crystal packing. The interaction mode between the patches might give a clue to the binding of the neurotoxin on the membrane. The agkistrodotoxin molecules in the asymmetric unit form two tetramers and each tetramer exhibits a novel "dimer of dimers"-like structure. A molecule-spanning four-stranded antiparallel beta-sheet is formed by the beta-wings of two molecules within a tetramer.


    Related Citations: 
    • Crystal Structure of Agkistrodotoxin, a Phospholipase A2-Type Presynaptic Neurotoxin from Agkistrodon Halys Pallas
      Tang, L.,Zhou, Y.C.,Lin, Z.J.
      (1998) J.Mol.Biol. 282: 1


    Organizational Affiliation

    Academia Sinica, Beijing, 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
A, B, C, D, E, F, G, H
122Gloydius halysEC: 3.1.1.4
Find proteins for P14421 (Gloydius halys)
Go to UniProtKB:  P14421
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 108.950α = 90.00
b = 85.227β = 109.66
c = 71.054γ = 90.00
Software Package:
Software NamePurpose
XENGENdata collection
X-PLORphasing
X-PLORrefinement
XENGENdata scaling
XENGENdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-03-05
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance