2WBG

Structure of family 1 beta-glucosidase from Thermotoga maritima in complex with 3-imino-2-oxa-(+)-castanospermine

• PDB DOI: https://doi.org/10.2210/pdb2WBG/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-27 Released: 2009-04-14 
• Deposition Author(s): Aguilar, M., Gloster, T.M., Turkenburg, J.P., Garcia-Moreno, M.I., Ortiz Mellet, C., Davies, G.J., Garcia Fernandez, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.199 
• R-Value Work: 0.153 
• R-Value Observed: 0.156 

Literature

Glycosidase Inhibition by Ring-Modified Castanospermine Analogues: Tackling Enzyme Selectivity by Inhibitor Tailoring.

Aguilar-Moncayo, M., Gloster, T.M., Turkenburg, J.P., Garcia-Moreno, M.I., Ortiz Mellet, C., Davies, G.J., Garcia Fernandez, J.M.

(2009) Org Biomol Chem 7: 2738

• PubMed: 19532990 
• DOI: https://doi.org/10.1039/b906968b
• Primary Citation of Related Structures:  
  2WBG, 2WC3, 2WC4


• PubMed Abstract: 
  

  Synthesis of a panel of iso(thio)urea-type ring-modified castanospermine analogues bearing a freely mutarotating pseudoanomeric hydroxyl group results in tight-binding beta-glucosidase inhibitors with unusual binding signatures; the presence of an N-octyl substituent imparts a remarkable anomeric selectivity, promoting strong binding of the appropriate beta-anomer by the beta-glucosidase.

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Organizational Affiliation: 

Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Profesor García González 1, 41012, Sevilla, (Spain).

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 217.09 kDa 
• Atom Count: 16,641 
• Modelled Residue Count: 1,772 
• Deposited Residue Count: 1,872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GLUCOSIDASE A	A, B, C, D	468	Thermotoga maritima	Mutation(s): 0  EC: 3.2.1.21
UniProt
Find proteins for Q08638 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q08638  Go to UniProtKB:  Q08638

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LGS	E [auth A], F [auth B], G [auth C], I [auth D]	(3Z,5S,6R,7S,8R,8aR)-3-(octylimino)hexahydro[1,3]oxazolo[3,4-a]pyridine-5,6,7,8-tetrol C15 H28 N2 O5 QJILQIWQVOAQBB-KRIYVDMXSA-N
ACT	H [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
LGS	PDBBind:  2WBG	Ki: 3.52e+4 (nM) from 1 assay(s)
	Binding MOAD:  2WBG	Ki: 3.52e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.199 
• R-Value Work: 0.153 
• R-Value Observed: 0.156 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.989	α = 90
b = 73.187	β = 94.03
c = 138.085	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-14 
Deposition Author(s): Aguilar, M., Gloster, T.M., Turkenburg, J.P., Garcia-Moreno, M.I., Ortiz Mellet, C., Davies, G.J., Garcia Fernandez, J.M.

Revision History  

• Version 1.0: 2009-04-14
  Type: Initial release
  
• Version 1.1: 2012-08-01
  Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description