Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 56.94 kDa 
• Atom Count: 3933 
• Modelled Residue Count: 449 
• Deposited Residue Count: 495 
• Unique protein chains: 1

1OPK

Structural basis for the auto-inhibition of c-Abl tyrosine kinase

• PDB DOI: 10.2210/pdb1OPK/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2003-03-06 Released: 2003-04-08 
• Deposition Author(s): Nagar, B., Hantschel, O., Young, M.A., Scheffzek, K., Veach, D., Bornmann, W., Clarkson, B., Superti-Furga, G., Kuriyan, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.221 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Literature

Structural basis for the autoinhibition of c-Abl tyrosine kinase

Nagar, B., Hantschel, O., Young, M.A., Scheffzek, K., Veach, D., Bornmann, W., Clarkson, B., Superti-Furga, G., Kuriyan, J.

(2003) Cell 112: 859-871

• PubMed: 12654251 
• DOI: 10.1016/s0092-8674(03)00194-6
• Primary Citation of Related Structures:  
  1OPJ, 1OPK, 1OPL


• PubMed Abstract: 
  

c-Abl is normally regulated by an autoinhibitory mechanism, the disruption of which leads to chronic myelogenous leukemia. The details of this mechanism have been elusive because c-Abl lacks a phosphotyrosine residue that triggers the assembly of the autoinhibited form of the closely related Src kinases by internally engaging the SH2 domain. Crystal structures of c-Abl show that the N-terminal myristoyl modification of c-Abl 1b binds to the kinase domain and induces conformational changes that allow the SH2 and SH3 domains to dock onto it. Autoinhibited c-Abl forms an assembly that is strikingly similar to that of inactive Src kinases but with specific differences that explain the differential ability of the drug STI-571/Gleevec/imatinib (STI-571) to inhibit the catalytic activity of Abl, but not that of c-Src.

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Related Citations: 

• A myristoyl/phosphotyrosine switch regulates c-Abl
  Hantschel, O., Nagar, B., Guettler, S., Kretzschmar, J., Dorey, K., Kuriyan, J., Superti-Furga, G.
  (2003) Cell 112: 845

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Organizational Affiliation: 

Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase ABL1	A	495	Mus musculus	Mutation(s): 1  Gene Names: Abl1, Abl EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
UniProt
Find proteins for P00520 (Mus musculus) Explore P00520  Go to UniProtKB:  P00520

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P16	C [auth A]	6-(2,6-DICHLOROPHENYL)-2-{[3-(HYDROXYMETHYL)PHENYL]AMINO}-8-METHYLPYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE C21 H16 Cl2 N4 O2 ZIQFYVPVJZEOFS-UHFFFAOYSA-N
MYR	B [auth A]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P16	BindingDB:  1OPK	IC50: 2.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.221 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.328	α = 90
b = 123.943	β = 90
c = 74.798	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-03-06 
• Released Date: 2003-04-08 
Deposition Author(s): Nagar, B., Hantschel, O., Young, M.A., Scheffzek, K., Veach, D., Bornmann, W., Clarkson, B., Superti-Furga, G., Kuriyan, J.

Revision History  

• Version 1.0: 2003-04-08
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations