Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 206538.41 
• Atom Count: 7292 
• Residue Count: 1832 
• Unique protein chains: 1

5M7S

Structure of human O-GlcNAc hydrolase with bound transition state analog ThiametG

• DOI: 10.2210/pdb5M7S/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2016-10-28 Released: 2017-03-29 
• Deposition Author(s): Roth, C., Chan, S., Offen, W.A., Hemsworth, G.R., Willems, L.I., King, D., Varghese, V., Britton, R., Vocadlo, D.J., Davies, G.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council; Canadian Institutes of Health Research 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.232 
• R-Value Work: 0.207 

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

• PubMed: 28346405 
• DOI: 10.1038/nchembio.2358
• Primary Citation of Related Structures:  
  5M7U, 5M7T, 5M7R


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Protein O-GlcNAcase	A, B	916	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NHT	A, B	(3AR,5R,6S,7R,7AR)-2-(ETHYLAMINO)-5-(HYDROXYMETHYL)-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL C9 H16 N2 O4 S PPAIMZHKIXDJRN-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.232 
• R-Value Work: 0.207 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 101.908	α = 90.00
b = 101.908	β = 90.00
c = 282.799	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
Aimless	data scaling
REFMAC	phasing
XDS	data reduction
REFMAC	refinement
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-10-28 
• Released Date: 2017-03-29 
• Deposition Author(s): Roth, C., Chan, S., Offen, W.A., Hemsworth, G.R., Willems, L.I., King, D., Varghese, V., Britton, R., Vocadlo, D.J., Davies, G.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/K003836/1
Canadian Institutes of Health Research	Canada	MOP-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