1W9B

S. alba myrosinase in complex with carba-glucotropaeolin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history


Literature

The glucosinolate-myrosinase system. New insights into enzyme-substrate interactions by use of simplified inhibitors.

Bourderioux, A.Lefoix, M.Gueyrard, D.Tatibouet, A.Cottaz, S.Arzt, S.Burmeister, W.P.Rollin, P.

(2005) Org Biomol Chem 3: 1872-1879

  • DOI: 10.1039/b502990b
  • Primary Citation of Related Structures:  
    1W9D, 1W9B

  • PubMed Abstract: 
  • Myrosinase, a thioglucoside glucohydrolase, is the only enzyme able to hydrolyse glucosinolates, a unique family of molecules bearing an anomeric O-sulfated thiohydroximate function. Non-hydrolysable myrosinase inhibitors have been devised and studied for their biological interaction ...

    Myrosinase, a thioglucoside glucohydrolase, is the only enzyme able to hydrolyse glucosinolates, a unique family of molecules bearing an anomeric O-sulfated thiohydroximate function. Non-hydrolysable myrosinase inhibitors have been devised and studied for their biological interaction. Diverse modifications of the O-sulfate moiety did not result in a significant inhibitory effect, whereas replacing the D-glucopyrano residue by its carba-analogue allowed inhibition to take place. X-Ray experiments carried out after soaking allowed for the first time inclusion of a non-hydrolysable inhibitor inside the enzymatic pocket. Structural tuning of the aglycon part in its pocket is being used as a guide for the development of simplified and more potent inhibitors.


    Related Citations: 
    • High Resolution X-Ray Crystallography Shows that Ascorbate is a Cofactor for Myrosinase and Substitutes for the Function of the Catalytic Base
      Burmeister, W.P., Cottaz, S., Rollin, P., Vasella, A., Henrissat, B.
      (2000) J Biol Chem 275: 39385

    Organizational Affiliation

    Institut de Chimie Organique et Analytique (ICOA), UMR 6005, Université d'Orléans, BP 6759, F-45067, Orléans Cedex 2, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCOSIDASEA [auth M]501Sinapis albaMutation(s): 0 
EC: 3.2.3.1 (PDB Primary Data), 3.2.1.147 (UniProt)
UniProt
Find proteins for P29736 (Sinapis alba)
Explore P29736 
Go to UniProtKB:  P29736
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth A], E [auth D]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth B]5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G06206UV
GlyCosmos:  G06206UV
GlyGen:  G06206UV
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G26295XE
GlyCosmos:  G26295XE
GlyGen:  G26295XE
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CGT (Subject of Investigation/LOI)
Query on CGT

Download Ideal Coordinates CCD File 
L [auth M]CARBA-GLUCOTROPAEOLIN
C15 H21 N O8 S2
LZDZCEOFJWRJIA-GGASBGQWSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
F [auth M], G [auth M], H [auth M], I [auth M], J [auth M], K [auth M]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
O [auth M], P [auth M], Q [auth M], R [auth M]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M, S [auth M], T [auth M]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
N [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CGT Binding MOAD:  1W9B IC50: 9.90e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.3α = 90
b = 137.2β = 90
c = 80.6γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-12-19
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary