2WC3 | pdb_00002wc3

Structure of family 1 beta-glucosidase from Thermotoga maritima in complex with 3-imino-2-oxa-(+)-8-epi-castanospermine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.249 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AM3Click on this verticalbar to view details

This is version 1.3 of the entry. See complete history. 


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

  • 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.

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

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-GLUCOSIDASE A
A, B, C, D
468Thermotoga maritimaMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08638
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.812α = 90
b = 73.965β = 108.49
c = 119.318γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AM3Click on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2012-08-01
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2017-07-12
    Changes: Data collection
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description