3ZJ7

Crystal structure of strictosidine glucosidase in complex with inhibitor-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.3109/14756366.2014.949252
  • Primary Citation of Related Structures:  
    3ZJ6, 3ZJ7, 3ZJ8

  • 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)- 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
A, B
532Rauvolfia serpentinaMutation(s): 0 
EC: 3.2.1.105
UniProt
Find proteins for Q8GU20 (Rauvolfia serpentina)
Explore Q8GU20 
Go to UniProtKB:  Q8GU20
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GU20
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C1K
Query on C1K

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(1R,2S,3S,4R,5R)-4-(cyclohexylamino)-5-(hydroxymethyl)cyclopentane-1,2,3-triol
C12 H23 N O4
ODXSPHZWZNYGJU-KNZXXDILSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.219α = 90
b = 159.219β = 90
c = 110.974γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2015-02-11
    Changes: Database references
  • Version 1.2: 2015-07-22
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description