6CDT | pdb_00006cdt

Structure of Human Anaplastic Lymphoma Kinase Domain

• PDB DOI: https://doi.org/10.2210/pdb6CDT/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera aff. frugiperda 2 RZ-2014
• Mutation(s): No 


• Deposited: 2018-02-09 Released: 2019-02-20 
• Deposition Author(s): McTigue, M., Deng, Y.L., Liu, W., Brooun, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.226 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Reviving B-Factors: Activating ALK Mutations Increase Protein Dynamics of the Unphosphorylated Kinase.

Johnson, T.W., Bolanos, B., Brooun, A., Gallego, R.A., Gehlhaar, D., Jalaie, M., McTigue, M., Timofeevski, S.

(2018) ACS Med Chem Lett 9: 872-877

• PubMed: 30258533 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00348
• Primary Citation Related Structures: 
  6CDT


• PubMed Abstract: 
  

  Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase that can become oncogenic by activating mutations or overexpression. Full kinetic characterization of both phosphorylated and nonphosphorylated wildtype and mutant ALK kinase domain was done. Our structure-based drug design programs directed at ALK allowed us to interrogate whether X-ray crystallography data could be used to support the hypothesis that activation of ALK by mutation occurs due to increased protein dynamics. Crystallographic B-factors were converted to normalized B-factors, which allowed analysis of wildtype ALK, ALK-C1156Y, and ALK-L1196M. This data suggests that mobility of the P-loop, αC-helix, and activation loop (A-loop) may be important in catalytic activity increases, with or without phosphorylation. Both molecular dynamics simulations and hydrogen-deuterium exchange experimental data corroborated the normalized B-factors data.

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Organizational Affiliation: 
• Pfizer Worldwide Research and Development, La Jolla Oncology, 10770 Science Center Drive, San Diego, California 92121, United States.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.91 kDa 
• Atom Count: 2,575 
• Modeled Residue Count: 292 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALK tyrosine kinase receptor	A	327	Homo sapiens	Mutation(s): 0  Gene Names: ALK EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM73 (Homo sapiens) Explore Q9UM73  Go to UniProtKB:  Q9UM73
PHAROS:  Q9UM73 GTEx:  ENSG00000171094

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.226 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.028	α = 90
b = 57.472	β = 90
c = 104.729	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): McTigue, M., Deng, Y.L., Liu, W., Brooun, A.

Revision History  

• Version 1.0: 2019-02-20
  Type: Initial release
  
• Version 1.1: 2019-02-27
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description