Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Macromolecule Content

• Total Structure Weight: 33207.35 
• Atom Count: 2152 
• Residue Count: 291 
• Unique protein chains: 1

2Y6M

Crystal structure of EphA4 kinase domain

• DOI: 10.2210/pdb2Y6M/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2011-01-25 Released: 2011-11-02 
• Deposition Author(s): Farenc, C.J.A., Celie, P.H.N., Siegal, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.203 
• R-Value Work: 0.175 

Literature

Crystal Structure of the Epha4 Protein Tyrosine Kinase Domain in the Apo- and Dasatinib-Bound State.

Farenc, C.J.A., Celie, P.H.N., Tensen, C.P., Siegal, G.

(2011) FEBS Lett. 585: 3593

• PubMed: 22036717 
• DOI: 10.1016/j.febslet.2011.10.028
• Primary Citation of Related Structures:  
  2Y6O


• PubMed Abstract: 
  

The Eph family of receptor tyrosine kinases regulates diverse cellular processes while the over-expression of a member of this family, EphA4, has been reported in a variety of malignant carcinomas. To gain insight into molecular mechanisms and to facilitate structure-based inhibitor design, we solved the crystal structure of the native EphA4 kinase domain in both the apo and dasatinib bound forms. Analysis of the two structures provides insight into structural features of inhibitor binding and revealed a hydrophobic back-pocket in the ATP- binding site of EphA4 which was previously unidentified. The structures suggest a route towards development of novel and specific inhibitors.

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Organizational Affiliation: 

Protein Chemistry Group, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
EPHRIN TYPE-A RECEPTOR 4	A	291	Mus musculus	Mutation(s): 0  Gene Names: Epha4 (Sek, Sek1) EC: 2.7.10.1
Find proteins for Q03137 (Mus musculus) Go to UniProtKB:  Q03137

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.203 
• R-Value Work: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 32.513	α = 90.00
b = 91.045	β = 90.00
c = 97.738	γ = 90.00

Software Package:

Software Name	Purpose
AMoRE	phasing
XDS	data scaling
XDS	data reduction
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-01-25 
• Released Date: 2011-11-02 
• Deposition Author(s): Farenc, C.J.A., Celie, P.H.N., Siegal, G.

Revision History 

• Version 1.0: 2011-11-02
  Type: Initial release
• Version 1.1: 2011-11-09
  Type: Database references
• Version 1.2: 2011-11-23
  Type: Database references