5JAW

Structure of a beta galactosidase with inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Towards broad spectrum activity-based glycosidase probes: synthesis and evaluation of deoxygenated cyclophellitol aziridines.

Schroder, S.P., van de Sande, J.W., Kallemeijn, W.W., Kuo, C.L., Artola, M., van Rooden, E.J., Jiang, J., Beenakker, T.J.M., Florea, B.I., Offen, W.A., Davies, G.J., Minnaard, A.J., Aerts, J.M.F.G., Codee, J.D.C., van der Marel, G.A., Overkleeft, H.S.

(2017) Chem. Commun. (Camb.) 53: 12528-12531

  • DOI: 10.1039/c7cc07730k

  • PubMed Abstract: 

    • Activity-based protein profiling has emerged as a powerful tool for visualizing glycosidases in complex biological samples. Several configurational cyclophellitol isomers have been shown to display high selectivity as probes for glycosidases processi ...

    Activity-based protein profiling has emerged as a powerful tool for visualizing glycosidases in complex biological samples. Several configurational cyclophellitol isomers have been shown to display high selectivity as probes for glycosidases processing substrates featuring the same configuration. Here, a set of deoxygenated cyclophellitols are presented which enable inter-class profiling of β-glucosidases and β-galactosidases.

    Organizational Affiliation: 

    Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands. h.s.overkleeft@chem.leidenuniv.nl.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galactosidase, putative, bgl35A
A, B, C, D, E, F, G, H
550Cellvibrio japonicus (strain Ueda107)Mutation(s): 0 
Gene Names: bgl35A
EC: 3.2.1.23
Find proteins for B3PBE0 (Cellvibrio japonicus (strain Ueda107))
Go to UniProtKB:  B3PBE0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT
Download SDF File 
Download CCD File 
E
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
UUU
Query on UUU
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
(1S,2S,3S,4S,5R,6R)-5-amino-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol
C7 H15 N O5
SWVTZDDSAFUTKS-OUIVRQFQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.197 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 99.168α = 90.15
b = 115.660β = 90.11
c = 115.935γ = 90.11
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
REFMACrefinement
DIALSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-04-12 
  • Released Date: 2017-05-10 
  • Deposition Author(s): Offen, W., Davies, G.
Funding OrganizationLocationGrant Number
United Kingdom--

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2018-01-10
    Type: Database references