3ZJ7

Crystal structure of strictosidine glucosidase in complex with inhibitor-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ligand Structures of Synthetic Deoxa-Pyranosylamines with Raucaffricine and Strictosidine Glucosidases Provide Structural Insights Into Their Binding and Inhibitory Behaviours.

Xia, L.Lin, H.Staniek, A.Panjikar, S.Ruppert, M.Hilgers, P.Williardt, J.Rajendran, C.Wang, M.Warzecha, H.Jager, V.Stockigt, J.

(2015) J.Enzyme.Inhib.Med.Chem. 30: 472

  • DOI: 10.3109/14756366.2014.949252
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Insight into the structure and inhibition mechanism of O-β-d-glucosidases by deoxa-pyranosylamine type inhibitors is provided by X-ray analysis of complexes between raucaffricine and strictosidine glucosidases and N-(cyclohexylmethyl)-, N-(cyclohexyl ...

    Insight into the structure and inhibition mechanism of O-β-d-glucosidases by deoxa-pyranosylamine type inhibitors is provided by X-ray analysis of complexes between raucaffricine and strictosidine glucosidases and N-(cyclohexylmethyl)-, N-(cyclohexyl)- and N-(bromobenzyl)-β-d-gluco-1,5-deoxa-pyranosylamine. All inhibitors anchored exclusively in the catalytic active site by competition with appropriate enzyme substrates. Thus facilitated prospective elucidation of the binding networks with residues located at <3.9 Å distance will enable the development of potent inhibitors suitable for the production of valuable alkaloid glucosides, raucaffricine and strictosidine, by means of synthesis in Rauvolfia serpentina cell suspension cultures.


    Organizational Affiliation

    Department of Urology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University , Hangzhou , China .




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
A, B
532Rauvolfia serpentinaMutation(s): 0 
Gene Names: SGR1
EC: 3.2.1.105
Find proteins for Q8GU20 (Rauvolfia serpentina)
Go to UniProtKB:  Q8GU20
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C1K
Query on C1K

Download SDF File 
Download CCD File 
A, B
(1R,2S,3S,4R,5R)-4-(cyclohexylamino)-5-(hydroxymethyl)cyclopentane-1,2,3-triol
C12 H23 N O4
ODXSPHZWZNYGJU-KNZXXDILSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.258 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 159.219α = 90.00
b = 159.219β = 90.00
c = 110.974γ = 90.00
Software Package:
Software NamePurpose
Auto-Rickshawphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2015-02-11
    Type: Database references
  • Version 1.2: 2015-07-22
    Type: Database references