1XXS

Structural insights for fatty acid binding in a Lys49 phospholipase A2: crystal structure of myotoxin II from Bothrops moojeni complexed with stearic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.170 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural insights for fatty acid binding in a Lys49-phospholipase A(2): crystal structure of myotoxin II from Bothrops moojeni complexed with stearic acid

Watanabe, L.Soares, A.M.Ward, R.J.Fontes, M.R.Arni, R.K.

(2005) Biochimie 87: 161-167

  • DOI: https://doi.org/10.1016/j.biochi.2004.11.005
  • Primary Citation of Related Structures:  
    1XXS

  • PubMed Abstract: 

    The crystal structure of dimeric Lys49-phospholipase A2 myotoxin-II from Bothrops moojeni (MjTX-II) co-crystallized with stearic acid (C(18)H(36)O(2)) has been determined at a resolution of 1.8 A. The electron density maps permitted the unambiguous inclusion of six stearic acid molecules in the refinement. Two stearic acid molecules could be located in the substrate-binding cleft of each monomer in positions, which favor the interaction of their carboxyl groups with active site residues. The way of binding of stearic acids to this Lys49-PLA(2)s is analogous to phospholipids and transition state analogues to catalytically active PLA(2)s. Two additional stearic acid molecules were located at the dimer interface region, defining a hitherto unidentified acyl-binding site on the protein surface. The strictly conserved Lys122 for Lys49-PLA(2)s may play a fundamental role for stabilization of legend-protein complex. The comparison of MjTX-II/satiric acid complex with other Lys-PLA(2)s structures whose putative fatty acids were located at their active site is also analysed. Molecular details of the stearic acid/protein interactions provide insights to binding in group I/II PLA(2)s, and to the possible interactions of Lys49-PLA(2)s with target membranes.


  • Organizational Affiliation

    Departamento de Física, IBILCE, UNESP, S. J. do Rio Preto-SP, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phospholipase A2 homolog 2
A, B
122Bothrops moojeniMutation(s): 0 
EC: 3.1.1.4
UniProt
Find proteins for Q9I834 (Bothrops moojeni)
Explore Q9I834 
Go to UniProtKB:  Q9I834
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I834
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
STE
Query on STE

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
K [auth B]
L [auth B]
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B]
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
I [auth B],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.18α = 90
b = 88.71β = 90
c = 51.09γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-29
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-04-03
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description