1ON8

Crystal structure of mouse alpha-1,4-N-acetylhexosaminyltransferase (EXTL2) with UDP and GlcUAb(1-3)Galb(1-O)-naphthalenelmethanol an acceptor substrate analog

• PDB DOI: https://doi.org/10.2210/pdb1ON8/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-02-27 Released: 2003-04-22 
• Deposition Author(s): Pedersen, L.C., Dong, J., Taniguchi, F., Kitagawa, H., Krahn, J.M., Pedersen, L.G., Sugahara, K., Negishi, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.254 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 

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)

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.55 kDa 
• Atom Count: 4,393 
• Modelled Residue Count: 527 
• Deposited Residue Count: 586 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1,4-N-acetylhexosaminyltransferase EXTL2	A, B	293	Mus musculus	Mutation(s): 0  Gene Names: EXTL2 OR EXTR2 EC: 2.4.1
UniProt
Find proteins for Q9ES89 (Mus musculus) Explore Q9ES89  Go to UniProtKB:  Q9ES89

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranuronic acid-(1-3)-beta-D-galactopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G99041PQ GlyCosmos:  G99041PQ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	F [auth A], I [auth B]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
EDO	G [auth A], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	E [auth A], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.254 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.157	α = 90
b = 125.157	β = 90
c = 83.692	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-22 
Deposition Author(s): Pedersen, L.C., Dong, J., Taniguchi, F., Kitagawa, H., Krahn, J.M., Pedersen, L.G., Sugahara, K., Negishi, M.

Revision History  

• Version 1.0: 2003-04-22
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-16
  Changes: Data collection, Database references, Refinement description, Structure summary