5JAW

Structure of a beta galactosidase with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1039/c7cc07730k
  • Primary Citation of Related Structures:  
    5JAW

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactosidase, putative, bgl35A
A, B, C, D, E
A, B, C, D, E, F, G, H
550Cellvibrio japonicus Ueda107Mutation(s): 0 
Gene Names: bgl35ACJA_2707
EC: 3.2.1.23
UniProt
Find proteins for B3PBE0 (Cellvibrio japonicus (strain Ueda107))
Explore B3PBE0 
Go to UniProtKB:  B3PBE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3PBE0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UUU
Query on UUU

Download Ideal Coordinates CCD File 
GA [auth F]
I [auth A]
JA [auth G]
M [auth B]
NA [auth H]
GA [auth F],
I [auth A],
JA [auth G],
M [auth B],
NA [auth H],
Q [auth C],
V [auth D],
Z [auth E]
(1S,2S,3S,4S,5R,6R)-5-amino-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol
C7 H15 N O5
SWVTZDDSAFUTKS-OUIVRQFQSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
FA [auth E]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
DA [auth E]
EA [auth E]
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth E],
HA [auth F],
IA [auth F],
J [auth A],
K [auth A],
KA [auth G],
L [auth A],
LA [auth G],
MA [auth G],
N [auth B],
O [auth B],
OA [auth H],
P [auth B],
PA [auth H],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
W [auth D],
X [auth D],
Y [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.168α = 90.15
b = 115.66β = 90.11
c = 115.935γ = 90.11
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2018-01-10
    Changes: Database references
  • Version 1.2: 2020-03-11
    Changes: Derived calculations, Refinement description
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary