4NXS | pdb_00004nxs

Crystal structure of human alpha-galactosidase A in complex with 1-deoxygalactonojirimycin-pFPhT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.232 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Molecular Basis of 1-Deoxygalactonojirimycin Arylthiourea Binding to Human alpha-Galactosidase A: Pharmacological Chaperoning Efficacy on Fabry Disease Mutants.

Yu, Y.Mena-Barragan, T.Higaki, K.Johnson, J.L.Drury, J.E.Lieberman, R.L.Nakasone, N.Ninomiya, H.Tsukimura, T.Sakuraba, H.Suzuki, Y.Nanba, E.Mellet, C.O.Garcia Fernandez, J.M.Ohno, K.

(2014) ACS Chem Biol 9: 1460-1469

  • DOI: https://doi.org/10.1021/cb500143h
  • Primary Citation Related Structures: 
    4NXS

  • PubMed Abstract: 

    Fabry disease (FD) is an X-linked lysosomal storage disorder caused by mutations in the GLA gene often leading to missense α-galactosidase A (α-Gal A) variants that undergo premature endoplasmic reticulum-associated degradation due to folding defects. We have synthesized and characterized a new family of neutral amphiphilic pharmacological chaperones, namely 1-deoxygalactonojirimycin-arylthioureas (DGJ-ArTs), capable of stabilizing α-Gal A and restoring trafficking. Binding to the enzyme is reinforced by a strong hydrogen bond involving the aryl-N'H thiourea proton and the catalytic aspartic acid acid D231 of α-Gal A, as confirmed by a 2.55 Å resolution cocrystal structure. Selected candidates enhanced α-Gal A activity and ameliorate globotriaosylceramide (Gb3) accumulation and autophagy impairments in FD cell cultures. Moreover, they acted synergistically with the proteostasis regulator 4-phenylbutyric acid, appearing to be promising leads as pharmacological chaperones for FD.


  • Organizational Affiliation
    • Division of Functional Genomics, Research Center for Bioscience and Technology, Tottori University , Yonago 683-8503, Japan.

Macromolecule Content 

  • Total Structure Weight: 93.64 kDa 
  • Atom Count: 6,536 
  • Modeled Residue Count: 781 
  • Deposited Residue Count: 796 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-galactosidase A
A, B
398Homo sapiensMutation(s): 0 
Gene Names: GLA
EC: 3.2.1.22
UniProt & NIH Common Fund Data Resources
Find proteins for P06280 (Homo sapiens)
Explore P06280 
Go to UniProtKB:  P06280
PHAROS:  P06280
GTEx:  ENSG00000102393 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06280
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P06280-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2OZ

Query on 2OZ



Download:Ideal Coordinates CCD File
J [auth A],
O [auth B]
(2R,3S,4R,5S)-N-(4-fluorophenyl)-3,4,5-trihydroxy-2-(hydroxymethyl)piperidine-1-carbothioamide
C13 H17 F N2 O4 S
WPBCEOLJVINCLL-NOOOWODRSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
M [auth B],
N [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
2OZ BindingDB:  4NXS IC50: min: 43, max: 340 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.232 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.783α = 90
b = 90.783β = 90
c = 217.382γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Structure summary