2WC4

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMF
Query on AMF
Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
H [auth C],
L [auth D]		(3Z,5S,6R,7S,8R,8aS)-3-(octylimino)hexahydro[1,3]thiazolo[3,4-a]pyridine-5,6,7,8-tetrol
C15 H28 N2 O4 S
HXWFEIXEWVGTGU-KRIYVDMXSA-N
EDO
Query on EDO
Download Ideal Coordinates CCD File 
F [auth A]
J [auth C]
M [auth D]
N [auth D]
O [auth D]
F [auth A],
J [auth C],
M [auth D],
N [auth D],
O [auth D],
P [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT
Download Ideal Coordinates CCD File 
I [auth C]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA
Download Ideal Coordinates CCD File 
K [auth C],
Q [auth D]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
AMF PDBBind:  2WC4 Kd: 5100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.872α = 90
b = 73.287β = 94.17
c = 137.979γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description