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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.192

Literature

Macromolecules
Sequence Display for 1ON8

Classification: TRANSFERASE

Total Structure Weight: 68583.55

Macromolecule Entities
Molecule Chains Length Organism Details
Alpha-1,4-N-acetylhexosaminyltransferase EXTL2 A, B 293 Mus musculus EC#: 2.4.1.223 IUBMB
Fragment: catalytic domain
Gene Name(s): Extl2 Extr2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
UDP
Query on UDP

A, B URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BDP
Query on BDP

A, B BETA-D-GLUCOPYRANURONIC ACID
D-GLUCURONIC ACID (Synonym)
C6 H10 O7
AEMOLEFTQBMNLQ-QIUUJYRFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAL
Query on GAL

A, B BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.192
  • Space Group: P 4 21 2

Unit Cell:

Length (Å) Angle (°)
a = 125.16 α = 90.00
b = 125.16 β = 90.00
c = 83.69 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-02-27
  • 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

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Non-polymer description, Version format compliance

  • Version 1_3: 2017-10-11

    Type: Refinement description