Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 107.25 kDa 
• Atom Count: 5,892 
• Modelled Residue Count: 857 
• Deposited Residue Count: 999 
• Unique protein chains: 1

 3EO3

Crystal structure of the N-acetylmannosamine kinase domain of human GNE protein

• PDB DOI:  https://doi.org/10.2210/pdb3EO3/pdb

• Classification: Isomerase, Transferase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-26 Released: 2008-10-07 
• Deposition Author(s): Nedyalkova, L., Tong, Y., Rabeh, W.M., Hong, B., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.245 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

Crystal structure of the N-acetylmannosamine kinase domain of GNE.

Tong, Y., Tempel, W., Nedyalkova, L., Mackenzie, F., Park, H.W.

(2009) PLoS One 4: e7165-e7165

• PubMed: 19841673 
• DOI: https://doi.org/10.1371/journal.pone.0007165
• Primary Citation of Related Structures:  
  3EO3


• PubMed Abstract: 
  

UDP-GlcNAc 2-epimerase/ManNAc 6-kinase, GNE, is a bi-functional enzyme that plays a key role in sialic acid biosynthesis. Mutations of the GNE protein cause sialurea or autosomal recessive inclusion body myopathy/Nonaka myopathy. GNE is the only human protein that contains a kinase domain belonging to the ROK (repressor, ORF, kinase) family.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase	A, B, C	333	Homo sapiens	Mutation(s): 0  Gene Names: GNE, GLCNE EC: 5.1.3.14 (PDB Primary Data), 2.7.1.60 (PDB Primary Data), 3.2.1.183 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y223 (Homo sapiens) Explore Q9Y223  Go to UniProtKB:  Q9Y223
PHAROS:  Q9Y223

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], G [auth B], I [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	E [auth A], F [auth A], H [auth B], J [auth C]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.245 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 3₁ 2 1
• Diffraction Data: https://doi.org/10.18430/m33eo3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.946	α = 90
b = 127.946	β = 90
c = 127.247	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-07 
Deposition Author(s): Nedyalkova, L., Tong, Y., Rabeh, W.M., Hong, B., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-10-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description