2CBU

Beta-glucosidase from Thermotoga maritima in complex with castanospermine

• PDB DOI: https://doi.org/10.2210/pdb2CBU/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-01-09 Released: 2006-02-03 
• Deposition Author(s): Gloster, T.M., Davies, G.J., Madsen, R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.237 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

Dissection of Conformationally Restricted Inhibitors Binding to a Beta-Glucosidase.

Gloster, T.M., Madsen, R., Davies, G.J.

(2006) Chembiochem 7: 738

• PubMed: 16628756 
• DOI: https://doi.org/10.1002/cbic.200600005
• Primary Citation of Related Structures:  
  2CBU, 2CBV

---

Organizational Affiliation: 

Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, UK.

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: 108.42 kDa 
• Atom Count: 8,225 
• Modelled Residue Count: 881 
• Deposited Residue Count: 936 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GLUCOSIDASE A	A, B	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CTS	C [auth A], F [auth B]	CASTANOSPERMINE C8 H15 N O4 JDVVGAQPNNXQDW-TVNFTVLESA-N
ACT	D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CTS	PDBBind:  2CBU	Kd: 2100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.237 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.076	α = 90
b = 94.521	β = 90
c = 113.28	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-03 
Deposition Author(s): Gloster, T.M., Davies, G.J., Madsen, R.

Revision History  

• Version 1.0: 2006-02-03
  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, Derived calculations, Other, Refinement description