2CEQ

Beta-glycosidase from Sulfolobus solfataricus in complex with glucoimidazole

• PDB DOI: https://doi.org/10.2210/pdb2CEQ/pdb

• Classification: HYDROLASE
• Organism(s): Saccharolobus solfataricus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-02-10 Released: 2006-09-27 
• Deposition Author(s): Gloster, T.M., Moracci, M., Vasella, A., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.215 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Starting Model: experimental

Literature

Structural, Kinetic, and Thermodynamic Analysis of Glucoimidazole-Derived Glycosidase Inhibitors.

Gloster, T.M., Roberts, S., Perugino, G., Rossi, M., Moracci, M., Panday, N., Terinek, M., Vasella, A., Davies, G.J.

(2006) Biochemistry 45: 11879

• PubMed: 17002288 
• DOI: https://doi.org/10.1021/bi060973x
• Primary Citation of Related Structures:  
  2CEQ, 2CER, 2CES, 2CET


• PubMed Abstract: 
  

  Inhibition of glycosidases has great potential in the quest for highly potent and specific drugs to treat diseases such as diabetes, cancer, and viral infections. One of the most effective ways of designing such compounds is by mimicking the transition state. Here we describe the structural, kinetic, and thermodynamic dissection of binding of two glucoimidazole-derived compounds, which are among the most potent glycosidase inhibitors reported to date, with two family 1 beta-glycosidases. Provocatively, while inclusion of the phenethyl moiety improves binding by a factor of 20-80-fold, this does not appear to result from better noncovalent interactions with the enzyme; instead, improved affinity may be derived from significantly better entropic contributions to binding displayed by the phenethyl-substituted imidazole compound.

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Organizational Affiliation: 

Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 114.22 kDa 
• Atom Count: 9,121 
• Modelled Residue Count: 978 
• Deposited Residue Count: 978 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GALACTOSIDASE	A, B	489	Saccharolobus solfataricus	Mutation(s): 0  EC: 3.2.1.23
UniProt
Find proteins for P22498 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore P22498  Go to UniProtKB:  P22498

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GIM	E [auth A], I [auth B]	GLUCOIMIDAZOLE C8 H13 N2 O4 RZRDQZQPTISYKY-MVIOUDGNSA-O
ACT	C [auth A], D [auth A], F [auth B], G [auth B], H [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
GIM	PDBBind:  2CEQ	Ki: 53 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.215 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.927	α = 90
b = 167.927	β = 90
c = 93.42	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-27 
Deposition Author(s): Gloster, T.M., Moracci, M., Vasella, A., Davies, G.J.

Revision History  

• Version 1.0: 2006-09-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description