5M7T

Structure of human O-GlcNAc hydrolase with PugNAc type inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and functional insight into human O-GlcNAcase.

Roth, C.Chan, S.Offen, W.A.Hemsworth, G.R.Willems, L.I.King, D.T.Varghese, V.Britton, R.Vocadlo, D.J.Davies, G.J.

(2017) Nat. Chem. Biol. 13: 610-612

  • DOI: 10.1038/nchembio.2358
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • O-GlcNAc hydrolase (OGA) removes O-linked N-acetylglucosamine (O-GlcNAc) from a myriad of nucleocytoplasmic proteins. Through co-expression and assembly of OGA fragments, we determined the three-dimensional structure of human OGA, revealing an unusua ...

    O-GlcNAc hydrolase (OGA) removes O-linked N-acetylglucosamine (O-GlcNAc) from a myriad of nucleocytoplasmic proteins. Through co-expression and assembly of OGA fragments, we determined the three-dimensional structure of human OGA, revealing an unusual helix-exchanged dimer that lays a structural foundation for an improved understanding of substrate recognition and regulation of OGA. Structures of OGA in complex with a series of inhibitors define a precise blueprint for the design of inhibitors that have clinical value.


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry University of York, York, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein O-GlcNAcase
A, B
916Homo sapiensMutation(s): 0 
Gene Names: OGA (HEXC, KIAA0679, MEA5, MGEA5)
EC: 3.2.1.169
Find proteins for O60502 (Homo sapiens)
Go to UniProtKB:  O60502
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDV
Query on GDV

Download SDF File 
Download CCD File 
A, B
(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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.203 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.146α = 90.00
b = 101.146β = 90.00
c = 283.289γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K003836/1
Canadian Institutes of Health ResearchCanadaMOP-123341

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Database references
  • Version 1.2: 2017-05-24
    Type: Database references
  • Version 1.3: 2017-08-30
    Type: Author supporting evidence