Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 94.70 kDa 
• Atom Count: 5180 
• Residue Count: 628 
• Unique protein chains: 1

4XEY

Crystal structure of an SH2-kinase domain construct of c-Abl tyrosine kinase

• DOI: 10.2210/pdb4XEY/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-25 Released: 2015-04-01 
• Deposition Author(s): Lorenz, S., Deng, P., Kuriyan, J.
• Funding Organization(s): Leukemia & Lymphoma Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.259 
• R-Value Work: 0.231 
• R-Value Observed: 0.232 

Literature

Crystal structure of an SH2-kinase construct of c-Abl and effect of the SH2 domain on kinase activity.

Lorenz, S., Deng, P., Hantschel, O., Superti-Furga, G., Kuriyan, J.

(2015) Biochem J 468: 283-291

• PubMed: 25779001 
• DOI: 10.1042/BJ20141492
• Primary Citation of Related Structures:  
  4XEY


• PubMed Abstract: 
  

Constitutive activation of the non-receptor tyrosine kinase c-Abl (cellular Abelson tyrosine protein kinase 1, Abl1) in the Bcr (breakpoint cluster region)-Abl1 fusion oncoprotein is the molecular cause of chronic myeloid leukaemia (CML). Recent studies have indicated that an interaction between the SH2 (Src-homology 2) domain and the N-lobe (N-terminal lobe) of the c-Abl kinase domain (KD) has a critical role in leukaemogenesis [Grebien et al. (2011) Cell 147, 306-319; Sherbenou et al. (2010) Blood 116, 3278-3285]. To dissect the structural basis of this phenomenon, we studied c-Abl constructs comprising the SH2 and KDs in vitro. We present a crystal structure of an SH2-KD construct bound to dasatinib, which contains the relevant interface between the SH2 domain and the N-lobe of the KD. We show that the presence of the SH2 domain enhances kinase activity moderately and that this effect depends on contacts in the SH2/N-lobe interface and is abrogated by specific mutations. Consistently, formation of the interface decreases slightly the association rate of imatinib with the KD. That the effects are small compared with the dramatic in vivo consequences suggests an important function of the SH2-N-lobe interaction might be to help disassemble the auto-inhibited conformation of c-Abl and promote processive phosphorylation, rather than substantially stimulate kinase activity.

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Organizational Affiliation: 

*California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, U.S.A.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase ABL1	A, B	408	Homo sapiens	Mutation(s): 0  Gene Names: ABL1, ABL, JTK7 EC: 2.7.10.2
Find proteins for P00519 (Homo sapiens) Explore P00519  Go to UniProtKB:  P00519
NIH Common Fund Data Resources
PHAROS  P00519 GTEx  ENSG00000097007

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1N1	A, B	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE C22 H26 Cl N7 O2 S ZBNZXTGUTAYRHI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.259 
• R-Value Work: 0.231 
• R-Value Observed: 0.232 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.118	α = 90
b = 125.449	β = 90
c = 56.232	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-12-25 
• Released Date: 2015-04-01 
Deposition Author(s): Lorenz, S., Deng, P., Kuriyan, J.

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Funding Organization	Location	Grant Number
Leukemia & Lymphoma Society	United States	7393-06

Revision History 

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2015-06-03
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy