5VVX

Structural Investigations of the Substrate Specificity of Human O-GlcNAcase

• PDB DOI: https://doi.org/10.2210/pdb5VVX/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-05-21 Released: 2017-09-27 
• Deposition Author(s): Li, B., Jiang, J., Li, H., Hu, C.-W.
• Funding Organization(s): UW-Madison

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.282 
• R-Value Work: 0.200 
• R-Value Observed: 0.204 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 118.78 kDa 
• Atom Count: 7,104 
• Modelled Residue Count: 861 
• Deposited Residue Count: 1,034 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein O-GlcNAcase	A, B [auth C]	504	Homo sapiens	Mutation(s): 1  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
Lamin B1	C [auth B], D	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P20700 (Homo sapiens) Explore P20700  Go to UniProtKB:  P20700
PHAROS:  P20700 GTEx:  ENSG00000113368

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth B], F [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.282 
• R-Value Work: 0.200 
• R-Value Observed: 0.204 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.922	α = 90
b = 96.222	β = 114.56
c = 89.653	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): Li, B., Jiang, J., Li, H., Hu, C.-W.

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Funding Organization	Location	Grant Number
UW-Madison	United States	--

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary