3ZJ6

Crystal of Raucaffricine Glucosidase in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.164 

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.


    Related Citations: 
    • Structures of Alkaloid Biosynthetic Glucosidases Decode Substrate Specificity.
      Xia, L.,Ruppert, M.,Wang, M.,Panjikar, S.,Lin, H.,Rajendran, C.,Barleben, L.,Stockigt, J.
      (2012) Acs Chem.Biol. 7: 226


    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
RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE
A, B
540Rauvolfia serpentinaMutation(s): 0 
Gene Names: RG (VGT)
EC: 3.2.1.125
Find proteins for Q9SPP9 (Rauvolfia serpentina)
Go to UniProtKB:  Q9SPP9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
VM2
Query on VM2

Download SDF File 
Download CCD File 
A, B
(1R,2S,3S,4R,5R)-4-(cyclohexylmethylamino)-5-(hydroxymethyl)cyclopentane-1,2,3-triol
C13 H25 N O4
PETSRUBXPDOLKZ-QWQWKMKNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.164 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 103.146α = 90.00
b = 127.954β = 90.00
c = 215.204γ = 90.00
Software Package:
Software NamePurpose
Auto-Rickshawphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2015-02-04
    Type: Database references
  • Version 1.2: 2015-07-22
    Type: Database references