5FKY Hydrolase date Oct 20, 2015
title Structure Of A Hydrolase Bound With An Inhibitor
authors N.Cekic, J.E.Heinonen, K.A.Stubbs, C.Roth, E.J.Mceachern, G.J.Dav D.J.Vocadlo
compound source
Molecule: O-Glcnacase Bt_4395
Chain: A, B
Synonym: Beta-N-Acetylglucosaminidase, Beta-N-Acetylhexosam Beta-Hexosaminidase, Hexosaminidase B, N-Acetyl-Beta-Glucos Glycoside Hydrolase;
Ec: 3.2.1.169
Engineered: Yes
 Organism_scientific: Bacteroides Thetaiotaomicron
Organism_taxid: 818
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
symmetry Space Group: P 1
R_factor 0.211 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
51.440 93.690 99.020 104.07 94.18 102.97
method X-Ray Diffractionresolution 1.80 Å
ligand 2J4, GOL enzyme Hydrolase E.C.3.2.1.169 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceAnalysis of transition state mimicry by tight binding aminothiazoline inhibitors provides insight into catalysis by human O-GlcNAcase., Cekic N, Heinonen JE, Stubbs KA, Roth C, He Y, Bennet AJ, McEachern EJ, Davies GJ, Vocadlo DJ, Chem Sci. 2016 Jun 1;7(6):3742-3750. doi: 10.1039/c6sc00370b. Epub 2016 Feb 15. PMID:29997861
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (459 Kb) [Save to disk]
  • Biological Unit Coordinates (5fky.pdb1.gz) 227 Kb
  • Biological Unit Coordinates (5fky.pdb2.gz) 229 Kb
  • LPC: Ligand-Protein Contacts for 5FKY
  • CSU: Contacts of Structural Units for 5FKY
  • Structure Factors (1853 Kb)
  • Retrieve 5FKY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5FKY from S2C, [Save to disk]
  • Re-refined 5fky structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5FKY 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 5FKY
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5fky] [5fky_A] [5fky_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5FKY
  • Community annotation for 5FKY at PDBWiki (http://pdbwiki.org)

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