2X05

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EXO-BETA-D-GLUCOSAMINIDASE
A, B
1,032Amycolatopsis orientalisMutation(s): 0 
EC: 3.2.1.165
UniProt
Find proteins for Q56F26 (Amycolatopsis orientalis)
Explore Q56F26 
Go to UniProtKB:  Q56F26
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56F26
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X05
Query on X05

Download Ideal Coordinates CCD File 
C [auth A],
M [auth B]
AMINO-CASTANOSPERMINE
C8 H16 N2 O3
LKBIVYWSUHFIBP-TVNFTVLESA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
X05 Binding MOAD:  2X05 Ki: 610 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.12α = 90
b = 121.8β = 90.51
c = 91.56γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MERGEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-15
    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