2X09

Inhibition of the exo-beta-D-glucosaminidase CsxA by a glucosamine- configured castanospermine and an amino-australine analogue

• PDB DOI: https://doi.org/10.2210/pdb2X09/pdb

• Classification: HYDROLASE
• Organism(s): Amycolatopsis orientalis
• Expression System: Streptomyces lividans TK24
• Mutation(s): No 


• Deposited: 2009-12-07 Released: 2010-02-09 
• Deposition Author(s): Pluvinage, B., Ghinet, M.G., Brzezinski, R., Boraston, A.B., Stubbs, K.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.240 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

Inhibition of the Exo-Beta-D-Glucosaminidase Csxa by a Glucosamine-Configured Castanospermine and an Amino-Australine Analogue.

Pluvinage, B., Ghinet, M.G., Brzezinski, R., Boraston, A.B., Stubbs, K.A.

(2009) Org Biomol Chem 7: 4169

• PubMed: 19795054 
• DOI: https://doi.org/10.1039/b913235j
• Primary Citation of Related Structures:  
  2X05, 2X09


• PubMed Abstract: 
  

  The synthesis of amino-derivatives of castanospermine and australine and their characterisation as inhibitors of the exo-beta-D-glucosaminidase CsxA through enzyme kinetics and X-ray structural analysis is described.

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Organizational Affiliation: 

Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC, Canada V8W 3P6.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 221.98 kDa 
• Atom Count: 14,500 
• Modelled Residue Count: 1,702 
• Deposited Residue Count: 2,064 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXO-BETA-D-GLUCOSAMINIDASE	A, B	1,032	Amycolatopsis orientalis	Mutation(s): 0  EC: 3.2.1.165
UniProt
Find proteins for Q56F26 (Amycolatopsis orientalis) Explore Q56F26  Go to UniProtKB:  Q56F26

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X09	C [auth A], F [auth B]	AMINO-AUSTRALINE C8 H16 N2 O3 RTYGUSZVNGAYPW-OZRXBMAMSA-N
CD	D [auth A], E [auth A], G [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
X09	PDBBind:  2X09	Ki: 1.75e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.240 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.75	α = 90
b = 121.95	β = 90.65
c = 92.05	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MERGE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Pluvinage, B., Ghinet, M.G., Brzezinski, R., Boraston, A.B., Stubbs, K.A.

Revision History  

• Version 1.0: 2010-02-09
  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: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description