2EAC Hydrolase date Jan 31, 2007
title Crystal Structure Of 1,2-A-L-Fucosidase From Bifidobacterium Bifidum In Complex With Deoxyfuconojirimycin
authors M.Nagae, A.Tsuchiya, T.Katayama, K.Yamamoto, S.Wakatsuki, R.Kato
compound source
Molecule: Alpha-Fucosidase
Chain: A, B
Fragment: Catalytic Domain
Synonym: Afca 1,2a-L-Fucosidase
Ec: 3.2.1.63
Engineered: Yes
Organism_scientific: Bifidobacterium Bifidum
Organism_taxid: 1681
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex4t-1
symmetry Space Group: P 1 21 1
R_factor 0.150 R_Free 0.198
crystal
cell
length a length b length c angle alpha angle beta angle gamma
90.668 111.702 98.346 90.00 95.31 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CA, DFU enzyme Hydrolase E.C.3.2.1.63 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural Basis of the Catalytic Reaction Mechanism of Novel 1,2-{alpha}-L-Fucosidase from Bifidobacterium bifidum., Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, Kato R, J Biol Chem. 2007 Jun 22;282(25):18497-509. Epub 2007 Apr 25. PMID:17459873
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (309 Kb) [Save to disk]
  • Biological Unit Coordinates (2eac.pdb1.gz) 154 Kb
  • Biological Unit Coordinates (2eac.pdb2.gz) 154 Kb
  • LPC: Ligand-Protein Contacts for 2EAC
  • CSU: Contacts of Structural Units for 2EAC
  • Likely Quarternary Molecular Structure file(s) for 2EAC
  • Structure Factors (2473 Kb)
  • Retrieve 2EAC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2EAC from S2C, [Save to disk]
  • Re-refined 2eac structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2EAC 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 2EAC
  • 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 2EAC, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2eac_B] [2eac_A] [2eac]
  • SWISS-PROT database: [Q6JV24]
  • Domain organization of [Q6JV24_9BIFI] by SWISSPFAM
  • Other resources with information on 2EAC
  • Community annotation for 2EAC 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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