5M7S

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

• PDB DOI: https://doi.org/10.2210/pdb5M7S/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 2.40 Å
• R-Value Free: 0.232 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

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: https://doi.org/10.1038/nchembio.2358
• Primary Citation of Related Structures:  
  5M7R, 5M7S, 5M7T, 5M7U


• 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.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 206.54 kDa 
• Atom Count: 7,318 
• Modelled Residue Count: 887 
• Deposited Residue Count: 1,832 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein O-GlcNAcase	A, B	916	Homo sapiens	Mutation(s): 0  Gene Names: MGEA5, HEXC, KIAA0679, MEA5 EC: 3.2.1.169 (PDB Primary Data), 3.2.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60502 (Homo sapiens) Explore O60502  Go to UniProtKB:  O60502
PHAROS:  O60502 GTEx:  ENSG00000198408

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHT	C [auth A], D [auth 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: 2.40 Å
• R-Value Free: 0.232 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.908	α = 90
b = 101.908	β = 90
c = 282.799	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2017-05-24
  Changes: Database references
• Version 1.3: 2017-08-30
  Changes: Author supporting evidence
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary