1OPL | pdb_00001opl

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 
    0.315 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.306 (Depositor), 0.276 (DCC) 
  • R-Value Observed: 
    0.306 (Depositor) 

Starting Models: experimental
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This is version 1.4 of the entry. See complete history

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

  • DOI: https://doi.org/10.1016/s0092-8674(03)00194-6
  • Primary Citation 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.


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

Macromolecule Content 

  • Total Structure Weight: 123.12 kDa 
  • Atom Count: 6,655 
  • Modeled Residue Count: 816 
  • Deposited Residue Count: 1,074 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
proto-oncogene tyrosine-protein kinase
A, B
537Homo sapiensMutation(s): 3 
Gene Names: Abl
EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00519 (Homo sapiens)
Explore P00519 
Go to UniProtKB:  P00519
PHAROS:  P00519
GTEx:  ENSG00000097007 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00519
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
P16 BindingDB:  1OPL IC50: min: 2.8, max: 8 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free:  0.315 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.306 (Depositor), 0.276 (DCC) 
  • R-Value Observed: 0.306 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.017α = 90
b = 273.384β = 90
c = 124.384γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-16
    Changes: Data collection, Refinement description