5M7U | pdb_00005m7u

Structure of human O-GlcNAc hydrolase with new iminocyclitol type inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5M7U/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 for Health Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.227 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

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 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.
Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 206.82 kDa 
• Atom Count: 7,462 
• Modeled Residue Count: 896 
• 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
XHA	C [auth A], D [auth B]	2-[(2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-[3-[3-(trifluoromethyl)phenyl]propyl]pyrrolidin-2-yl]-~{N}-methyl-ethanamide C18 H25 F3 N2 O4 CCWQIKVWFWMBMG-TXCZRRACSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.227 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.23	α = 90
b = 101.23	β = 90
c = 284.673	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
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 for 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: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary