6AL3

Lys49 PLA2 BPII derived from the venom of Protobothrops flavoviridis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

SDS-induced oligomerization of Lys49-phospholipase A2from snake venom.

Matsui, T.Kamata, S.Ishii, K.Maruno, T.Ghanem, N.Uchiyama, S.Kato, K.Suzuki, A.Oda-Ueda, N.Ogawa, T.Tanaka, Y.

(2019) Sci Rep 9: 2330-2330

  • DOI: 10.1038/s41598-019-38861-8
  • Primary Citation of Related Structures:  
    6AL3

  • PubMed Abstract: 
  • Phospholipase A 2 (PLA 2 ) is one of the representative toxic components of snake venom. PLA 2 s are categorized into several subgroups according to the amino acid at position 49, which comprises either Asp49, Lys49, Arg49 or Ser49 ...

    Phospholipase A 2 (PLA 2 ) is one of the representative toxic components of snake venom. PLA 2 s are categorized into several subgroups according to the amino acid at position 49, which comprises either Asp49, Lys49, Arg49 or Ser49. Previous studies suggested that the Lys49-PLA 2 assembles into an extremely stable dimer. Although the behavior on Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) under reducing or non-reducing conditions suggested the presence of intermolecular disulfide bonds, these bonds were not observed in the crystal structure of Lys49-PLA 2 . The reason for this discrepancy between the crystal structure and SDS-PAGE of Lys49-PLA 2 remains unknown. In this study, we analyzed a Lys49-PLA 2 homologue from Protobothrops flavoviridis (PflLys49-PLA 2 BPII), by biophysical analyses including X-ray crystallography, SDS-PAGE, native-mass spectrometry, and analytical ultracentrifugation. The results demonstrated that PflLys49-PLA 2 BPII spontaneously oligomerized in the presence of SDS, which is one of the strongest protein denaturants.


    Organizational Affiliation

    Japan Science and Technology Agency, PRESTO, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan. yoshikazu.tanaka@tohoku.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Basic phospholipase A2 BP-IIA, B, C, D122Protobothrops flavoviridisMutation(s): 0 
EC: 3.1.1.4
Membrane Entity: Yes 
UniProt
Find proteins for P0DJJ9 (Protobothrops flavoviridis)
Explore P0DJJ9 
Go to UniProtKB:  P0DJJ9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth B], F [auth B], G [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.227 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.9α = 90
b = 126.9β = 90
c = 64.88γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-06
    Changes: Data collection, Database references