Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.14 kDa 
• Atom Count: 5,238 
• Modelled Residue Count: 499 
• Deposited Residue Count: 501 
• Unique protein chains: 1

 2WXD

A MICROMOLAR O-SULFATED THIOHYDROXIMATE INHIBITOR BOUND TO PLANT MYROSINASE

• PDB DOI: 10.2210/pdb2WXD/pdb

• Classification: HYDROLASE
• Organism(s): Sinapis alba
• Mutation(s): No 


• Deposited: 2009-11-09 Released: 2010-02-09 
• Deposition Author(s): Besle, A., Burmeister, W.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.164 
• R-Value Work: 0.143 
• R-Value Observed: 0.144 

Literature

A Micromolar O-Sulfated Thiohydroximate Inhibitor Bound to Plant Myrosinase

Besle, A., Brazzolotto, X., Tatibouet, A., Cerniauskaite, D., Gallienne, E., Rollin, P., Burmeister, W.P.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 152

• PubMed: 20124710 
• DOI: 10.1107/S1744309109052865
• Primary Citation of Related Structures:  
  2WXD


• PubMed Abstract: 
  

The 1.6 A resolution structure of the micromolar competitive inhibitor S-(N,N-dimethylaminoethyl) phenylacetothiohydroximate-O-sulfate bound to Sinapis alba myrosinase, a plant thioglucosidase, is reported. Myrosinase and its substrates, the glucosinolates, are part of the plant's defence system. The sulfate group and the phenyl group of the inhibitor bind to the aglycon-binding site of the enzyme, whereas the N,N-dimethyl group binds to the glucose-binding site and explains the large improvement in binding affinity compared with previous compounds. The structure suggests ways to increase the potency and specificity of the compound by improving the interactions with the hydrophobic pocket of the aglycon-binding site.

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Related Citations: 

• A Simple O-Sulfated Thiohydroximate Molecule to be the First Micromolar Range Myrosinase Inhibitor
  Cerniauskaite, D., Gallienne, E., Karciauskaite, H., Farinha, A.S.F., Rousseau, J., Armand, S., Tatibouet, A., Sackus, A., Rollin, P.
  (2009) Tetrahedron Lett 50: 3302

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Organizational Affiliation: 

UJF-EMBL-CNRS UMI 3265, Unit of Virus Host Cell Interactions, BP 181, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MYROSINASE	A [auth M]	501	Sinapis alba	Mutation(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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B [auth A], C [auth B], F [auth E], G [auth F]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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-glucopyranose	D [auth C]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G06206UV GlyCosmos:  G06206UV GlyGen:  G06206UV

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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-glucopyranose	E [auth D]	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G26295XE GlyCosmos:  G26295XE GlyGen:  G26295XE

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E18	L [auth M]	2-(DIMETHYLAMINO)ETHYL (1Z)-2-PHENYL-N-(SULFOOXY)ETHANIMIDOTHIOATE C12 H18 N2 O4 S2 AJWBDCAFLSUABV-SEYXRHQNSA-N
NAG	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
SO4	N [auth M], O [auth M], P [auth M], Q [auth M], R [auth M], S [auth M], T [auth M]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	U [auth M], V [auth M], W [auth M], X [auth M]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	M	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
E18	Binding MOAD:  2WXD	IC50: 3300 (nM) from 1 assay(s)
	PDBBind:  2WXD	IC50: 3300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.164 
• R-Value Work: 0.143 
• R-Value Observed: 0.144 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.245	α = 90
b = 137.567	β = 90
c = 80.723	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Besle, A., Burmeister, W.P.

Revision History  

• Version 1.0: 2010-02-09
  Type: Initial release
  
• Version 1.1: 2012-04-04
  Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary