2J47 | pdb_00002j47

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.229 (Depositor) 
  • R-Value Work: 
    0.192 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1039/b612154c
  • Primary Citation 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.

    • Organizational Affiliation: 
    • Laboratorium für Organische Chemie, HCI H 317, ETH Zürich, CH-8093 Zürich, Switzerland. vasella@org.chem.ethz.ch

Macromolecule Content 

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

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLUCOSAMINIDASE716Bacteroides thetaiotaomicron VPI-5482Mutation(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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89ZI2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDV

Query on GDV


Download:Ideal Coordinates CCD File
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

Query on GOL


Download:Ideal Coordinates CCD File
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.229 (Depositor) 
  • R-Value Work:  0.192 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.426α = 90
b = 51.34β = 100.22
c = 85.474γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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