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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of agkistrodotoxin in an orthorhombic crystal form with six molecules per asymmetric unit.

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

(1999) Acta Crystallogr.,Sect.D 55: 1986-1996


  • PubMed Abstract: 
  • The structure of agkistrodotoxin crystallized under basic conditions has been determined at 2.8 A resolution by the molecular-replacement technique and refined to a crystallographic R factor of 0.194 and a free R factor of 0.260 with good stereochemi ...

    The structure of agkistrodotoxin crystallized under basic conditions has been determined at 2.8 A resolution by the molecular-replacement technique and refined to a crystallographic R factor of 0.194 and a free R factor of 0.260 with good stereochemistry. The molecular packing in the crystal differs from other PLA(2)s. The six molecules in the asymmetric unit form three dimers linked by Ca(2+) ions in a near-perfect six-ligand octahedral coordinating system. Extensive intermolecular hydrophobic interactions occur at the interfacial recognition site of each neurotoxin molecule, which provides an insight into phospholipase A(2)-membrane interactions. This hydrophobic interaction-induced molecular association along the interfacial recognition site suggests a self-protection mechanism of agkistrodotoxin.


    Organizational Affiliation

    National Laboratory of Biological Macromolecules, Institute of Biophysics, Academia Sinica, Beijing 100101, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AGKISTRODOTOXIN
A, B, C, D, E, F
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
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.750α = 90.00
b = 105.800β = 90.00
c = 110.030γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
SCALEPACKdata scaling
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance