2JIW

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.248
R-Value Work: 0.206
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1039/b709681j
Primary Citation of 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q89ZI2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEU Query on BEU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	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		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]