2JIW | pdb_00002jiw

Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with 2- Acetylamino-2-deoxy-1-epivalienamine

• PDB DOI: https://doi.org/10.2210/pdb2JIW/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-07-02 Released: 2007-08-07 
• Deposition Author(s): Dennis, R.J., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.248 (Depositor) 
• R-Value Work: 
  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

A 1-Acetamido Derivative of 6-Epi-Valienamine: An Inhibitor of a Diverse Group of Beta-N-Acetylglucosaminidases.

Scaffidi, A., Stubbs, K.A., Dennis, R.J., Taylor, E.J., Davies, G.J., Vocadlo, D.J., Stick, R.V.

(2007) Org Biomol Chem 5: 3013

• PubMed: 17728868 
• DOI: https://doi.org/10.1039/b709681j
• Primary Citation Related Structures: 
  2JIW


• PubMed Abstract: 
  

  The synthesis of an analogue of 6-epi-valienamine bearing an acetamido group and its characterisation as an inhibitor of beta-N-acetylglucosaminidases are described. The compound is a good inhibitor of both human O-GlcNAcase and human beta-hexosaminidase, as well as two bacterial beta-N-acetylglucosaminidases. A 3-D structure of the complex of Bacteroides thetaiotaomicron BtGH84 with the inhibitor shows the unsaturated ring is surprisingly distorted away from its favoured solution phase conformation and reveals potential for improved inhibitor potency.

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Organizational Affiliation: 
• Chemistry M313, School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, Australia.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 165.07 kDa 
• Atom Count: 10,470 
• Modeled Residue Count: 1,180 
• Deposited Residue Count: 1,432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-GLCNACASE BT_4395	A, B	716	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  EC: 3.2.1.52 (PDB Primary Data), 3.2.1.169 (UniProt)
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEU	C [auth A], D [auth B]	N-[(1S,2R,5R,6R)-2-AMINO-5,6-DIHYDROXY-4-(HYDROXYMETHYL)CYCLOHEX-3-EN-1-YL]ACETAMIDE C9 H16 N2 O4 WWUMIYBLWZAJTD-BZNPZCIMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.248 (Depositor) 
• R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.398	α = 104.97
b = 94.131	β = 94.09
c = 99.808	γ = 102.48

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-07 
Deposition Author(s): Dennis, R.J., Davies, G.J.

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Other