2VKH Toxin date Dec 19, 2007
title Crystal Structure Of The Catalytic Domain Of Lethal Toxin From Clostridium Sordellii In Complex With Udp-Glc And Calcium Ion
authors M.O.P.Ziegler, T.Jank, K.Aktories, G.E.Schulz
compound source
Molecule: Cytotoxin L
Chain: A, B, C
Fragment: Catalytic Domain, Residues 1-546
Synonym: Lethal Toxin
Engineered: Yes
Mutation: Yes
 Organism_scientific: Clostridium Sordellii
Organism_taxid: 1505
Strain: 6018
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.235 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.170 188.590 203.100 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.3 Å
ligand CA, UPG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceConformational Changes and Reaction of Clostridial Glycosylating Toxins., Ziegler MO, Jank T, Aktories K, Schulz GE, J Mol Biol. 2008 Jan 5;. PMID:18325534
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (277 Kb) [Save to disk]
  • Biological Unit Coordinates (2vkh.pdb1.gz) 92 Kb
  • Biological Unit Coordinates (2vkh.pdb2.gz) 92 Kb
  • Biological Unit Coordinates (2vkh.pdb3.gz) 93 Kb
  • LPC: Ligand-Protein Contacts for 2VKH
  • CSU: Contacts of Structural Units for 2VKH
  • Likely Quarternary Molecular Structure file(s) for 2VKH
  • Structure Factors (750 Kb)
  • Retrieve 2VKH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VKH from S2C, [Save to disk]
  • Re-refined 2vkh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2VKH 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.
    • Visual 3D analysis of 2VKH
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2VKH, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vkh_C] [2vkh_B] [2vkh_A] [2vkh]
  • SWISS-PROT database: [Q46342]
  • Belongs to the clostridial cytotoxin (cct) family according to TCDB.
  • Domain organization of [Q46342_CLOSO] by SWISSPFAM
    • Other resources with information on 2VKH
  • Community annotation for 2VKH at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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