3GVL Hydrolase date Mar 31, 2009
title Crystal Structure Of Endo-Neuraminidasenf
authors E.C.Schulz, A.Dickmanns, R.Ficner
compound source
Molecule: Endo-N-Acetylneuraminidase
Chain: A
Fragment: Residues 246-910
Synonym: Endo-Alpha-Sialidase, Gp17 Protein
Ec: 3.2.1.129
Engineered: Yes
Organism_scientific: Enterobacteria Phage K1f
Organism_common: Bacteriophage K1f
Organism_taxid: 344021
Gene: Sia, 17, 17.0
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: H 3
R_factor 0.169 R_Free 0.188
crystal
cell
length a length b length c angle alpha angle beta angle gamma
119.092 119.092 175.981 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.41 Å
ligand SIA, SLB enzyme Hydrolase E.C.3.2.1.129 BRENDA
Primary referenceStructural Basis for the Recognition and Cleavage of Polysialic Acid by the Bacteriophage K1F Tailspike Protein EndoNF., Schulz EC, Schwarzer D, Frank M, Stummeyer K, Muhlenhoff M, Dickmanns A, Gerardy-Schahn R, Ficner R, J Mol Biol. 2010 Mar 19;397(1):341-351. Epub 2010 Jan 22. PMID:20096705
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk]
  • Biological Unit Coordinates (3gvl.pdb1.gz) 407 Kb
  • LPC: Ligand-Protein Contacts for 3GVL
  • CSU: Contacts of Structural Units for 3GVL
  • Structure Factors (1487 Kb)
  • Retrieve 3GVL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GVL from S2C, [Save to disk]
  • Re-refined 3gvl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GVL 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 3GVL
  • 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 3GVL, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gvl] [3gvl_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3GVL
  • Community annotation for 3GVL 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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