2AOZ

Crystal structure of the myotoxin-II from Atropoides nummifer venom

• PDB DOI: https://doi.org/10.2210/pdb2AOZ/pdb

• Classification: TOXIN
• Organism(s): Atropoides nummifer
• Mutation(s): No 


• Deposited: 2005-08-15 Released: 2006-07-25 
• Deposition Author(s): Melo, C.C., Murakami, M.T., Angulo, Y., Lomonte, B., Arni, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.275 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Literature

Structure of myotoxin II, a catalytically inactive Lys49 phospholipase A2 homologue from Atropoides nummifer venom.

Murakami, M.T., Melo, C.C., Angulo, Y., Lomonte, B., Arni, R.K.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 423-426

• PubMed: 16682766 
• DOI: https://doi.org/10.1107/S1744309106010700
• Primary Citation of Related Structures:  
  2AOZ


• PubMed Abstract: 
  

  Lys49 snake-venom phospholipase A2 (PLA2) homologues are highly myotoxic proteins which, although lacking catalytic activity, possess the ability to disrupt biological membranes, inducing significant muscle-tissue loss and permanent disability in severely envenomed patients. Since the structural basis for their toxic activity is still only partially understood, the structure of myotoxin II, a monomeric Lys49 PLA2 homologue from Atropoides nummifer, has been determined at 2.08 angstroms resolution and the anion-binding site has been characterized.

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Organizational Affiliation: 

Department of Physics, IBILCE/UNESP, São José do Rio Preto-SP, Brazil.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.83 kDa 
• Atom Count: 1,022 
• Modelled Residue Count: 121 
• Deposited Residue Count: 121 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 homolog	A	121	Atropoides nummifer	Mutation(s): 0
UniProt
Find proteins for P82950 (Atropoides nummifer) Explore P82950  Go to UniProtKB:  P82950

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.275 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.939	α = 90
b = 68.939	β = 90
c = 64.069	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-25 
Deposition Author(s): Melo, C.C., Murakami, M.T., Angulo, Y., Lomonte, B., Arni, R.K.

Revision History  

• Version 1.0: 2006-07-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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