3ZJ6 | pdb_00003zj6

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), 0.179 (DCC) 
  • R-Value Work: 
    0.164 (Depositor) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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 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 .

Macromolecule Content 

  • Total Structure Weight: 122.82 kDa 
  • Atom Count: 7,939 
  • Modeled Residue Count: 938 
  • Deposited Residue Count: 1,080 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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), 0.179 (DCC) 
  • R-Value Work:  0.164 (Depositor) 
  • 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 


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