6Y6T

Mouse Galactocerebrosidase complexed with galacto-noeurostegine GNS at pH 4.6

• PDB DOI: https://doi.org/10.2210/pdb6Y6T/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-02-27 Released: 2021-01-13 
• Deposition Author(s): Deane, J.E., McLoughlin, J.
• Funding Organization(s): Royal Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.198 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 

Starting Model: experimental

Literature

The Bicyclic Form of galacto -Noeurostegine Is a Potent Inhibitor of beta-Galactocerebrosidase.

Viuff, A., Salamone, S., McLoughlin, J., Deane, J.E., Jensen, H.H.

(2021) ACS Med Chem Lett 12: 56-59

• PubMed: 33488964 
• DOI: https://doi.org/10.1021/acsmedchemlett.0c00377
• Primary Citation of Related Structures:  
  6Y6S, 6Y6T


• PubMed Abstract: 
  

  Competitive inhibitors of galactocerebrosidase (GALC) could be candidates for pharmacological chaperone therapy of patients with Krabbe disease. The known and selective nortropane-type iminosugar galacto -noeurostegine has been found to competitively inhibit GALC with K _i = 7 μM at pH 4.6, which is 330-fold more potent than the analogous deoxynoeurostegine. It was shown through X-ray protein crystallography that galacto -noeurostegine binds to the active site of GALC in its bicyclic form.

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Organizational Affiliation: 

Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 76.38 kDa 
• Atom Count: 5,460 
• Modelled Residue Count: 641 
• Deposited Residue Count: 654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactocerebrosidase	A	654	Mus musculus	Mutation(s): 0  Gene Names: Galc EC: 3.2.1.46
UniProt
Find proteins for P54818 (Mus musculus) Explore P54818  Go to UniProtKB:  P54818
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: P54818-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ODW (Subject of Investigation/LOI)	E [auth A]	(1~{R},2~{S},3~{S},4~{R},5~{R})-4-(hydroxymethyl)-8-azabicyclo[3.2.1]octane-1,2,3-triol C8 H15 N O4 NLSPHUUFXPUPJJ-GWVFRZDISA-N
NI	H [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CA	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ODW	BindingDB:  6Y6T	Ki: 7000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.198 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 250.83	α = 90
b = 250.83	β = 90
c = 77.897	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Deane, J.E., McLoughlin, J.

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Funding Organization	Location	Grant Number
Royal Society	United Kingdom	UF100371

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2021-02-03
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description