1JLT

Vipoxin Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of the neurotoxic complex vipoxin at 1.4 A resolution.

Banumathi, S.Rajashankar, K.R.Notzel, C.Aleksiev, B.Singh, T.P.Genov, N.Betzel, C.

(2001) Acta Crystallogr.,Sect.D 57: 1552-1559


  • PubMed Abstract: 
  • Vipoxin is a neurotoxic postsynaptic heterodimeric complex from the venom of Vipera ammodytes meridionalis, the most toxic snake in Europe. It consists of a basic and highly toxic phospholipase A(2) and an acidic non-toxic protein inhibitor. The two ...

    Vipoxin is a neurotoxic postsynaptic heterodimeric complex from the venom of Vipera ammodytes meridionalis, the most toxic snake in Europe. It consists of a basic and highly toxic phospholipase A(2) and an acidic non-toxic protein inhibitor. The two polypeptide chains have the same chain length and share 62% amino-acid identity. Vipoxin is a unique example of evolution of the catalytic and toxic phospholipase A(2) functions into inhibitory and non-toxic functions. The crystal structure of the complex has been determined by the molecular-replacement method and refined to 1.4 A resolution to an R factor of 18.2%. The complex formation decreases the accessible surface area of the two subunits by approximately 1480 A(2), which results in a reduction of toxicity and catalytic activity. The catalytic and substrate-binding sites of the vipoxin phospholipase A(2) are identical or similar to those of other group I/II enzymes. Two 2-methyl-2,4-pentanediol molecules are present in the hydrophobic channel close to the active site. The two subunits lack calcium ions. The negatively charged Asp49 of the phospholipase A(2), which participates in the Ca(2+)-binding sites of other snake-venom phospholipase A(2)s, is neutralized by the side chain of Lys69 from the inhibitor. Attempts have been made to identify the toxicity region and to explain the reduced catalytic activity and toxicity of the phospholipase A(2) subunit.


    Organizational Affiliation

    Institute of Medical Biochemistry and Molecular Biology, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2 INHIBITOR
A
122Vipera ammodytes meridionalisN/A
Find proteins for P04084 (Vipera ammodytes meridionalis)
Go to UniProtKB:  P04084
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
B
122Vipera ammodytes meridionalisEC: 3.1.1.4
Find proteins for P14420 (Vipera ammodytes meridionalis)
Go to UniProtKB:  P14420
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download SDF File 
Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.049α = 90.00
b = 54.708β = 90.00
c = 104.760γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
CNSrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Advisory, Refinement description
  • Version 1.4: 2018-01-31
    Type: Experimental preparation