1RGB | pdb_00001rgb

Phospholipase A2 from Vipera ammodytes meridionalis

• PDB DOI: https://doi.org/10.2210/pdb1RGB/pdb

• Classification: HYDROLASE
• Organism(s): Vipera ammodytes meridionalis
• Mutation(s): No 


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

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Experimental Data Snapshot

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

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

• PubMed: 15194511 
• DOI: https://doi.org/10.1016/j.bbrc.2004.05.106
• Primary Citation 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 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.

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Organizational Affiliation: 
• Institut für Biochemie und Molekularbiologie I, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.95 kDa 
• Atom Count: 3,892 
• Modeled Residue Count: 488 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2	A, B, C [auth K], D [auth L]	122	Vipera ammodytes meridionalis	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for P14420 (Vipera ammodytes meridionalis) Explore P14420  Go to UniProtKB:  P14420

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ELD	E [auth B], F [auth L]	(9E)-OCTADEC-9-ENAMIDE C18 H35 N O FATBGEAMYMYZAF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.568	α = 90
b = 82.67	β = 90
c = 119.469	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.4: 2024-10-30
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary