2YFN Hydrolase date Apr 07, 2011
title Galactosidase Domain Of Alpha-Galactosidase-Sucrose Kinase,
authors G.Sulzenbacher, L.Bruel, M.Tison-Cervera, A.Pujol, C.Nicoletti, J A.Galinier, D.Ropartz, M.Fons, F.Pompeo, T.Giardina
compound source
Molecule: Alpha-Galactosidase-Sucrose Kinase Agask
Chain: A
Ec: 3.2.1.22
Engineered: Yes
 Organism_scientific: Ruminococcus Gnavus E1
Organism_taxid: 935582
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: I 2 2 2
R_factor 0.130 R_Free 0.150
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.058 111.650 154.886 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.45 Å
ligand EDO, GOL, MG, PO4 enzyme Hydrolase E.C.3.2.1.22 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referencealpha-Galactosidase/Sucrose Kinase (AgaSK), a Novel Bifunctional Enzyme from the Human Microbiome Coupling Galactosidase and Kinase Activities., Bruel L, Sulzenbacher G, Cervera Tison M, Pujol A, Nicoletti C, Perrier J, Galinier A, Ropartz D, Fons M, Pompeo F, Giardina T, J Biol Chem. 2011 Nov 25;286(47):40814-23. Epub 2011 Sep 19. PMID:21931163
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (256 Kb) [Save to disk]
  • Biological Unit Coordinates (2yfn.pdb1.gz) 990 Kb
  • LPC: Ligand-Protein Contacts for 2YFN
  • CSU: Contacts of Structural Units for 2YFN
  • Structure Factors (3817 Kb)
  • Retrieve 2YFN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YFN from S2C, [Save to disk]
  • Re-refined 2yfn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2YFN 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 2YFN
  • 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 2YFN, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yfn] [2yfn_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 2YFN
  • Community annotation for 2YFN at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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