2WC4 | pdb_00002wc4

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

• PDB DOI: https://doi.org/10.2210/pdb2WC4/pdb

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


• Deposited: 2009-03-08 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: 1.70 Å
• R-Value Free: 
  0.213 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.167 (Depositor) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

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 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: 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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PQS (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 217.6 kDa 
• Atom Count: 16,543 
• Modeled 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMF	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	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	I [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	K [auth C], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.213 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.167 (Depositor) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.872	α = 90
b = 73.287	β = 94.17
c = 137.979	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: 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