5UHP

Crystal structure of the core catalytic domain of human O-GlcNAcase

• PDB DOI: https://doi.org/10.2210/pdb5UHP/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2017-01-11 Released: 2017-03-29 
• Deposition Author(s): Klein, D.J., Elsen, N.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.292 
• R-Value Work: 0.239 
• R-Value Observed: 0.242 

Literature

Crystal structure of the core catalytic domain of human O-GlcNAcase and molecular basis of activity and inhibition

Elsen, N.L., Patel, S.B., Ford, R.E., Hall, D.L., Hess, F., Kandula, H., Kornienko, M., Lumb, K.J., Reid, J., Selnick, H., Shipman, J.M., Sharma, S., Soisson, S.M., Klein, D.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 249.99 kDa 
• Atom Count: 13,813 
• Modelled Residue Count: 1,681 
• Deposited Residue Count: 2,196 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-GlcNAcase TIM-barrel domain	A, B, C, D	388	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
O-GlcNAcase stalk domain	E, F, G, H	161	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
GOL	I [auth A], J [auth B], K [auth C], L [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.292 
• R-Value Work: 0.239 
• R-Value Observed: 0.242 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.722	α = 77.27
b = 91.531	β = 62.81
c = 94.517	γ = 63.03

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Klein, D.J., Elsen, N.L.

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references