1W9B | pdb_00001w9b

S. alba myrosinase in complex with carba-glucotropaeolin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.191 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.175 (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 CGTClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

This is version 3.2 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: https://doi.org/10.1039/b502990b
  • Primary Citation of Related Structures:  
    1W9B, 1W9D

  • 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. 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.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29736
Glycosylation
Glycosylation Sites: 9
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth A],
E [auth D]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D 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
Glycosylation Resources
GlyTouCan:  G06206UV
GlyCosmos:  G06206UV
GlyGen:  G06206UV
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D 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
Glycosylation Resources
GlyTouCan:  G26295XE
GlyCosmos:  G26295XE
GlyGen:  G26295XE
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CGT
Query on CGT

Download Ideal Coordinates CCD File 
L [auth M]CARBA-GLUCOTROPAEOLIN
C15 H21 N O8 S2
LZDZCEOFJWRJIA-GGASBGQWSA-N
NAG
Query on NAG

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

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

Download Ideal Coordinates CCD File 
N [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.191 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
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 

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

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
  • Version 3.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 3.2: 2024-10-16
    Changes: Structure summary