5ABE

Structure of GH84 with ligand

• PDB DOI: https://doi.org/10.2210/pdb5ABE/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-05 Released: 2015-11-18 
• Deposition Author(s): Bergeron-Brlek, M., Goodwin-Tindall, J., Cekic, N., Varghese, V., Zandberg, W.F., Shan, X., Roth, C., Chan, S., Davies, G.J., Vocadlo, D.J., Britton, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.244 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Literature

A Convenient Approach to Stereoisomeric Iminocyclitols: Generation of Potent Brain-Permeable Oga Inhibitors.

Bergeron-Brlek, M., Goodwin-Tindall, J., Cekic, N., Roth, C., Zandberg, W.F., Shan, X., Varghese, V., Chan, S., Davies, G.J., Vocadlo, D.J., Britton, R.

(2015) Angew Chem Int Ed Engl 54: 15429

• PubMed: 26545827 
• DOI: https://doi.org/10.1002/anie.201507985
• Primary Citation of Related Structures:  
  5ABE, 5ABF, 5ABG, 5ABH


• PubMed Abstract: 
  

  Pyrrolidine-based iminocyclitols are a promising class of glycosidase inhibitors. Reported herein is a convenient epimerization strategy that provides direct access to a range of stereoisomeric iminocyclitol inhibitors of O-GlcNAcase (OGA), the enzyme responsible for catalyzing removal of O-GlcNAc from nucleocytoplasmic proteins. Structural details regarding the binding of these inhibitors to a bacterial homologue of OGA reveal the basis for potency. These compounds are orally available and permeate into rodent brain to increase O-GlcNAc, and should prove useful tools for studying the role of OGA in health and disease.

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Organizational Affiliation: 

Department of Chemistry, Simon Fraser University, Burnaby, British Columbia (Canada).

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 167.6 kDa 
• Atom Count: 11,263 
• Modelled Residue Count: 1,351 
• Deposited Residue Count: 1,452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-GLCNACASE BT_4395	A, B	726	Bacteroides thetaiotaomicron	Mutation(s): 0  EC: 3.2.1.169
UniProt
Find proteins for Q89ZI2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89ZI2  Go to UniProtKB:  Q89ZI2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XQO	C [auth A], E [auth B]	2-[(2S,3S,4R,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-pentyl-pyrrolidin-2-yl]-N-methyl-ethanamide C13 H26 N2 O4 NZYWNYJYZSBEBH-JULQROHOSA-N
CA	D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.244 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.572	α = 90
b = 159.605	β = 90
c = 223.121	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Bergeron-Brlek, M., Goodwin-Tindall, J., Cekic, N., Varghese, V., Zandberg, W.F., Shan, X., Roth, C., Chan, S., Davies, G.J., Vocadlo, D.J., Britton, R.

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2015-11-25
  Changes: Structure summary
• Version 1.2: 2016-01-27
  Changes: Database references
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other