1RGB

Phospholipase A2 from Vipera ammodytes meridionalis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Asp49 phospholipase A(2)-elaidoylamide complex: a new mode of inhibition.

Georgieva, D.N., Rypniewski, W., Gabdoulkhakov, A., Genov, N., Betzel, C.

(2004) Biochem Biophys Res Commun 319: 1314-1321

  • DOI: 10.1016/j.bbrc.2004.05.106
  • Primary Citation of Related Structures:  
    1RGB

  • PubMed Abstract: 

    • The inhibition of phospholipase A(2)s (PLA(2)s) is of pharmacological and therapeutic interest because these enzymes are involved in several inflammatory diseases. Elaidoylamide is a powerful inhibitor of a neurotoxic PLA(2) from the Vipera ammodytes ...

    The inhibition of phospholipase A(2)s (PLA(2)s) is of pharmacological and therapeutic interest because these enzymes are involved in several inflammatory diseases. Elaidoylamide is a powerful inhibitor of a neurotoxic PLA(2) from the Vipera ammodytes meridionalis venom. The X-ray structure of the enzyme-inhibitor complex reveals a new mode of Asp49 PLA(2) inhibition by a fatty acid hydrocarbon chain. The structure contains two identical homodimers in the asymmetric unit. In each dimer one subunit is rotated by 180 degrees with respect to the other and the two molecules are oriented head-to-tail. One molecule of elaidoylamide is bound simultaneously to the substrate binding sites of two associated neurotoxic phospholipase A(2) molecules. The inhibitor binds symmetrically to the hydrophobic channels of the two monomers. The structure can be used to design anti-inflammatory drugs.

    Organizational Affiliation: 

    Institut für Biochemie und Molekularbiologie I, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipase A2A, B, K, L122Vipera ammodytes meridionalisMutation(s): 0 
EC: 3.1.1.4
Find proteins for P14420 (Vipera ammodytes meridionalis)
Explore P14420 
Go to UniProtKB:  P14420
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ELD
Query on ELD
Download CCD File 
B, L
(9E)-OCTADEC-9-ENAMIDE
C18 H35 N O
FATBGEAMYMYZAF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.568α = 90
b = 82.67β = 90
c = 119.469γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2003-11-12 
  • Released Date: 2005-01-18 
    • Deposition Author(s): Georgieva, D.N.

Revision History 

  • Version 1.0: 2005-01-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-10-03
    Changes: Advisory, Data collection