2VK7 Hydrolase date Dec 17, 2007
title The Structure Of Clostridium Perfringens Nani Sialidase And Catalytic Intermediates
authors S.L.Newstead, J.A.Potter, J.C.Wilson, G.Xu, C.H.Chien, A.G.Watts, S.G.Withers, G.L.Taylor
compound source
Molecule: Exo-Alpha-Sialidase
Chain: A, B
Fragment: Catalytic Domain, Residues 243-694
Synonym: Sialidase
Ec: 3.2.1.18
Engineered: Yes
Organism_scientific: Clostridium Perfringens
Organism_taxid: 1502
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.131 R_Free 0.159
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.600 97.400 72.600 90.00 91.00 90.00
method X-Ray Diffractionresolution 1.20 Å
ligand CA, FSI enzyme Hydrolase E.C.3.2.1.18 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceThe Structure of Clostridium perfringens NanI Sialidase and Its Catalytic Intermediates., Newstead SL, Potter JA, Wilson JC, Xu G, Chien CH, Watts AG, Withers SG, Taylor GL, J Biol Chem. 2008 Apr 4;283(14):9080-8. Epub 2008 Jan 24. PMID:18218621
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (359 Kb) [Save to disk]
  • Biological Unit Coordinates (2vk7.pdb1.gz) 180 Kb
  • Biological Unit Coordinates (2vk7.pdb2.gz) 176 Kb
  • LPC: Ligand-Protein Contacts for 2VK7
  • CSU: Contacts of Structural Units for 2VK7
  • Likely Quarternary Molecular Structure file(s) for 2VK7
  • Structure Factors (2067 Kb)
  • Retrieve 2VK7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VK7 from S2C, [Save to disk]
  • Re-refined 2vk7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VK7 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 2VK7
  • 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 2VK7, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vk7_A] [2vk7] [2vk7_B]
  • SWISS-PROT database: [Q59310]
  • Domain organization of [Q59310_CLOPE] by SWISSPFAM
  • Other resources with information on 2VK7
  • Community annotation for 2VK7 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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