1MQB

Crystal Structure of Ephrin A2 (ephA2) Receptor Protein Kinase

• PDB DOI: https://doi.org/10.2210/pdb1MQB/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2002-09-16 Released: 2003-09-16 
• Deposition Author(s): Nowakowski, J., Cronin, C.N., McRee, D.E., Knuth, M.W., Nelson, C., Pavletich, N., Rogers, J., Sang, B.C., Scheibe, D.N., Swanson, R.V., Thompson, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.236 
• R-Value Observed: 0.236 

Starting Model: experimental

Literature

Structures of the Cancer Related Aurora-A, FAK and EphA2 Protein Kinases from Nanovolume Crystallography

Nowakowski, J., Cronin, C.N., McRee, D.E., Knuth, M.W., Nelson, C., Pavletich, N., Rogers, J., Sang, B.C., Scheibe, D.N., Swanson, R.V., Thompson, D.A.

(2003) Structure 10: 1659-1667

• PubMed: 12467573 
• DOI: https://doi.org/10.1016/s0969-2126(02)00907-3
• Primary Citation of Related Structures:  
  1MP8, 1MQ4, 1MQB


• PubMed Abstract: 
  

  Protein kinases are important drug targets in human cancers, inflammation, and metabolic diseases. This report presents the structures of kinase domains for three cancer-associated protein kinases: ephrin receptor A2 (EphA2), focal adhesion kinase (FAK), and Aurora-A. The expression profiles of EphA2, FAK, and Aurora-A in carcinomas suggest that inhibitors of these kinases may have inherent potential as therapeutic agents. The structures were determined from crystals grown in nanovolume droplets, which produced high-resolution diffraction data at 1.7, 1.9, and 2.3 A for FAK, Aurora-A, and EphA2, respectively. The FAK and Aurora-A structures are the first determined within two unique subfamilies of human kinases, and all three structures provide new insights into kinase regulation and the design of selective inhibitors.

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Organizational Affiliation: 

Syrrx, Inc., 10410 Science Center Drive, San Diego, CA 92121, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.58 kDa 
• Atom Count: 4,349 
• Modelled Residue Count: 528 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-A receptor 2	A, B	333	Homo sapiens	Mutation(s): 0  Gene Names: EphA2 EC: 2.7.1.112 (PDB Primary Data), 2.7.10.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P29317 (Homo sapiens) Explore P29317  Go to UniProtKB:  P29317
PHAROS:  P29317 GTEx:  ENSG00000142627

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A], D [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.236 
• R-Value Observed: 0.236 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.127	α = 90
b = 72.127	β = 90
c = 241.623	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-16 
Deposition Author(s): Nowakowski, J., Cronin, C.N., McRee, D.E., Knuth, M.W., Nelson, C., Pavletich, N., Rogers, J., Sang, B.C., Scheibe, D.N., Swanson, R.V., Thompson, D.A.

Revision History  

• Version 1.0: 2003-09-16
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description