3ZJ8

Crystal structure of strictosidine glucosidase in complex with inhibitor-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 
    0.237 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LR1Click on this verticalbar to view details

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
LR1
Query on LR1

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(1R,2S,3S,4R,5R)-4-[(4-bromophenyl)methylamino]-5-(hydroxymethyl)cyclopentane-1,2,3-triol
C13 H18 Br N O4
BSQKACVWQISROJ-QWQWKMKNSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.107α = 90
b = 159.107β = 90
c = 102.995γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LR1Click on this verticalbar to view details

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