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 1.2 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: 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
MoleculeChainsSequence LengthOrganismDetailsImage
EXO-BETA-D-GLUCOSAMINIDASEA, B1032Amycolatopsis orientalisMutation(s): 0 
Gene Names: csxA
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
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

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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