3ZJ6

Crystal of Raucaffricine Glucosidase in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.199 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.4 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
RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE
A, B
540Rauvolfia serpentinaMutation(s): 0 
EC: 3.2.1.125 (PDB Primary Data), 2.4.1.219 (UniProt)
UniProt
Find proteins for Q9SPP9 (Rauvolfia serpentina)
Explore Q9SPP9 
Go to UniProtKB:  Q9SPP9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SPP9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.199 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.146α = 90
b = 127.954β = 90
c = 215.204γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted VM2Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Database references
  • Version 1.2: 2015-07-22
    Changes: Database references
  • Version 1.3: 2019-07-17
    Changes: Data collection
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description