2BK2 Cytolytic Protein date Feb 08, 2005
title The Prepore Structure Of Pneumolysin, Obtained By Fitting The Alpha Carbon Trace Of Perfringolysin O Into A Cryo-Em Map
authors S.J.Tilley, E.V.Orlova, R.J.C.Gilbert, P.W.Andrew, H.R.Saibil
compound source
Molecule: Perfringolysin O
Chain: A
Engineered: Yes
Organism_scientific: Clostridium Perfringens
Expression_system: Escherichia Coli
symmetry Space Group: P 1
R_factor
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Cryo-Electron Microscopyresolution 28.00 Å
similarity Belongs to the thiol-activated cytolysin family.[Thiol_cytolysin]
subunit Forms oligomers in the host membrane.
Genes CPE0163, PFOA, PFOR, PFO (C. perfringens)
function Cholesterol is the receptor for the binding of these toxins to eukaryotic cell membranes. Is able to lyse cholesterol containing membranes. Sulfhydryl-activated toxin. Can be reversibly inactivated by oxidation.
Gene
Ontology
ChainFunctionProcessComponent
A
  • cholesterol binding
  • pathogenesis

  • Primary referenceStructural basis of pore formation by the bacterial toxin pneumolysin., Tilley SJ, Orlova EV, Gilbert RJ, Andrew PW, Saibil HR, Cell. 2005 Apr 22;121(2):247-56. PMID:15851031
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (18 Kb) [Save to disk]
  • Biological Unit Coordinates (2bk2.pdb1.gz) 300 Kb
  • CSU: Contacts of Structural Units for 2BK2
  • Likely Quarternary Molecular Structure file(s) for 2BK2
  • Retrieve 2BK2 in mmCIF format [Save to disk]
  • View 2BK2 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
  • Visual 3D analysis of 2BK2
  • Protein Explorer, Easier to use and more powerful than RasMol. (Win and Mac only)
  • Noncovalent Bond Finder displays the closest contacts to ligand or interface, reports distances, walks over water bridges.
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2BK2, from MSDmotif at EBI
  • Fold representative 2bk2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2bk2_A]
  • Other resources with information on 2BK2
  • InterPro: IPR001869
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2007
    Bioinformatics and Biological Computing
    Weizmann Institute of Science