2J47

Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with a imidazole-pugnac hybrid inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2J47/pdb

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


• Deposited: 2006-08-25 Released: 2006-10-03 
• Deposition Author(s): Dennis, R.J., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.229 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Inhibition of O-Glcnacase by a Gluco-Configured Nagstatin and a Pugnac-Imidazole Hybrid Inhibitor

Shanmugasundaram, B., Debowski, A.W., Dennis, R.J., Davies, G.J., Vocadlo, D.J., Vasella, A.

(2006) Chem Commun (Camb) 42: 4372

• PubMed: 17057847 
• DOI: https://doi.org/10.1039/b612154c
• Primary Citation of Related Structures:  
  2J47


• PubMed Abstract: 
  

  Synthesis of a PUGNAc-imidazole hybrid and its characterization as an inhibitor of human O-GlcNAcase through enzyme kinetics and X-ray structural analysis.

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Organizational Affiliation: 

Laboratorium für Organische Chemie, HCI H 317, ETH Zürich, CH-8093 Zürich, Switzerland. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 82.77 kDa 
• Atom Count: 5,019 
• Modelled Residue Count: 572 
• Deposited Residue Count: 716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOSAMINIDASE	A	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDV	B [auth A]	(5R,6R,7R,8S)-8-(ACETYLAMINO)-6,7-DIHYDROXY-5-(HYDROXYMETHYL)-N-PHENYL-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-2-CARBOXAMIDE C17 H21 N4 O5 WWSQBPPKQTUEDT-KBUPBQIOSA-O
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GDV	PDBBind:  2J47	Ki: 3900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.229 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.426	α = 90
b = 51.34	β = 100.22
c = 85.474	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-03 
Deposition Author(s): Dennis, R.J., Davies, G.J.

Revision History  

• Version 1.0: 2006-10-03
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description