Crystal structure of Lys49-Phospholipase A2 from Agkistrodon contortrix laticinctus, fatty acid bound form

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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A Molecular Mechanism for Lys49-Phospholipase A2 Activity Based on Ligand-induced Conformational Change.

Ambrosio, A.L.B.Nonato, M.C.Selistre de Araujo, H.S.Arni, R.Ward, R.J.Ownby, C.L.de Souza, D.H.F.Garratt, R.C.

(2005) J Biol Chem 280: 7326-7335

  • DOI: https://doi.org/10.1074/jbc.M410588200
  • Primary Citation of Related Structures:  
    1S8G, 1S8H, 1S8I

  • PubMed Abstract: 

    Agkistrodon contortrix laticinctus myotoxin is a Lys(49)-phospholipase A(2) (EC isolated from the venom of the serpent A. contortrix laticinctus (broad-banded copperhead). We present here three monomeric crystal structures of the myotoxin, obtained under different crystallization conditions. The three forms present notable structural differences and reveal that the presence of a ligand in the active site (naturally presumed to be a fatty acid) induces the exposure of a hydrophobic surface (the hydrophobic knuckle) toward the C terminus. The knuckle in A. contortrix laticinctus myotoxin involves the side chains of Phe(121) and Phe(124) and is a consequence of the formation of a canonical structure for the main chain within the region of residues 118-125. Comparison with other Lys(49)-phospholipase A(2) myotoxins shows that although the knuckle is a generic structural motif common to all members of the family, it is not readily recognizable by simple sequence analyses. An activation mechanism is proposed that relates fatty acid retention at the active site to conformational changes within the C-terminal region, a part of the molecule that has long been associated with Ca(2+)-independent membrane damaging activity and myotoxicity. This provides, for the first time, a direct structural connection between the phospholipase "active site" and the C-terminal "myotoxic site," justifying the otherwise enigmatic conservation of the residues of the former in supposedly catalytically inactive molecules.

  • Organizational Affiliation

    Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, USP, São Carlos-SP CEP 13560-970, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phospholipase A2 homolog121Agkistrodon contortrix laticinctusMutation(s): 0 
Find proteins for P49121 (Agkistrodon contortrix laticinctus)
Explore P49121 
Go to UniProtKB:  P49121
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49121
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.897α = 90
b = 81.897β = 90
c = 49.902γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-10
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description