5P2P | pdb_00005p2p

X-RAY STRUCTURE OF PHOSPHOLIPASE A2 COMPLEXED WITH A SUBSTRATE-DERIVED INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Observed: 
    0.189 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5P2P

This is version 1.4 of the entry. See complete history

Literature

X-ray structure of phospholipase A2 complexed with a substrate-derived inhibitor.

Thunnissen, M.M.Ab, E.Kalk, K.H.Drenth, J.Dijkstra, B.W.Kuipers, O.P.Dijkman, R.de Haas, G.H.Verheij, H.M.

(1990) Nature 347: 689-691

  • DOI: https://doi.org/10.1038/347689a0
  • Primary Citation Related Structures: 
    5P2P

  • PubMed Abstract: 

    Phospholipases A2 play a part in a number of physiologically important cellular processes such as inflammation, blood platelet aggregation and acute hypersensitivity. These processes are all initiated by the release of arachidonic acid from cell membranes which is catalysed by intracellular phospholipases A2 and followed by conversion of arachidonic acid to prostaglandins, leukotrienes or thromboxanes. An imbalance in the production of these compounds can lead to chronic inflammatory diseases such as rheumatoid arthritis and asthma. Inhibitors of phospholipase A2 might therefore act to reduce the effects of inflammation, so structural information about the binding of phospholipase A2 to its substrates could be helpful in the design of therapeutic drugs. The three-dimensional structure is not known for any intracellular phospholipase A2, but these enzymes share significant sequence homology with secreted phospholipases, for which some of the structures have been determined. Here we report the structure of a complex between an extracellular phospholipase A2 and a competitively inhibiting substrate analogue, which reveals considerable detail about the interaction and suggests a mechanism for catalysis by this enzyme.


  • Organizational Affiliation
    • Laboratory of Chemical Physics, University of Groningen, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 27.83 kDa 
  • Atom Count: 2,047 
  • Modeled Residue Count: 238 
  • Deposited Residue Count: 238 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOSPHOLIPASE A2
A, B
119Sus scrofaMutation(s): 0 
EC: 3.1.1.4
UniProt
Find proteins for P00592 (Sus scrofa)
Explore P00592 
Go to UniProtKB:  P00592
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00592
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.57α = 90
b = 62.44β = 90
c = 85.58γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1991-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-06-05
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2024-11-20
    Changes: Structure summary