|Entry||Database: PDB / ID: 2f4j|
|Title||Structure of the Kinase Domain of an Imatinib-Resistant Abl Mutant in Complex with the Aurora Kinase Inhibitor VX-680|
|Components||Proto-oncogene tyrosine-protein kinase ABL1|
|Keywords||TRANSFERASE / kinase / kinase inhibitor / abl|
|Function / homology|
Function and homology information
mitochondrial depolarization / positive regulation of actin filament binding / transitional one stage B cell differentiation / DNA conformation change / negative regulation of phospholipase C activity / regulation of extracellular matrix organization / activation of protein kinase C activity / positive regulation of interleukin-2 production => GO:0032743 / nicotinate-nucleotide adenylyltransferase activity / positive regulation blood vessel branching ...mitochondrial depolarization / positive regulation of actin filament binding / transitional one stage B cell differentiation / DNA conformation change / negative regulation of phospholipase C activity / regulation of extracellular matrix organization / activation of protein kinase C activity / positive regulation of interleukin-2 production => GO:0032743 / nicotinate-nucleotide adenylyltransferase activity / positive regulation blood vessel branching / alpha-beta T cell differentiation / B cell proliferation involved in immune response / regulation of modification of synaptic structure / positive regulation of microtubule binding / positive regulation of Wnt signaling pathway, planar cell polarity pathway / microspike assembly / neuroepithelial cell differentiation / cerebellum morphogenesis / collateral sprouting / B-1 B cell homeostasis / actin filament branching / circulatory system development => GO:0072359 / positive regulation of oxidoreductase activity / activated T cell proliferation / neuropilin binding / neuropilin signaling pathway / bubble DNA binding / regulation of Cdc42 protein signal transduction / negative regulation of protein serine/threonine kinase activity / regulation of T cell differentiation / negative regulation of ubiquitin-protein transferase activity / regulation of microtubule polymerization / negative regulation of BMP signaling pathway / regulation of actin cytoskeleton reorganization / mitogen-activated protein kinase binding / proline-rich region binding / sequence-specific double-stranded DNA binding / syntaxin binding / cellular response to dopamine / positive regulation of interferon-gamma production => GO:0032729 / negative regulation of cell-cell adhesion / DNA damage induced protein phosphorylation / negative regulation of cellular senescence / positive regulation of osteoblast proliferation / regulation of response to DNA damage stimulus / regulation of axon extension / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of cell migration involved in sprouting angiogenesis / cell leading edge / negative regulation of long-term synaptic potentiation / actin monomer binding / Bergmann glial cell differentiation / regulation of endocytosis / neuromuscular process controlling balance / positive regulation of focal adhesion assembly / positive regulation of actin cytoskeleton reorganization / positive regulation of substrate adhesion-dependent cell spreading / mismatch repair / regulation of hematopoietic stem cell differentiation / negative regulation of mitotic cell cycle / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / regulation of cell motility / endothelial cell migration / four-way junction DNA binding / positive regulation of stress fiber assembly / positive regulation of muscle cell differentiation / regulation of actin cytoskeleton organization / signal transduction in response to DNA damage / substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / regulation of autophagy / cellular protein modification process / post-embryonic development / spleen development / SH2 domain binding / negative regulation of I-kappaB kinase/NF-kappaB signaling / positive regulation of mitotic cell cycle / positive regulation of release of sequestered calcium ion into cytosol / thymus development / negative regulation of ERK1 and ERK2 cascade / protein kinase C binding / phosphotyrosine residue binding / ephrin receptor binding / integrin-mediated signaling pathway / neural tube closure / peptidyl-tyrosine autophosphorylation / actin cytoskeleton organization / non-specific protein-tyrosine kinase / establishment of protein localization / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / autophagy / SH3 domain binding / postsynapse / cell cycle arrest / cellular response to hydrogen peroxide / positive regulation of neuron death / intrinsic apoptotic signaling pathway in response to DNA damage / B cell receptor signaling pathway
Tyrosine-protein kinase, active site / SH3-like domain superfamily / F-actin binding / Protein kinase, ATP binding site / Tyrosine-protein kinase, catalytic domain / Tyrosine-protein kinase ABL1/transforming protein Abl / Serine-threonine/tyrosine-protein kinase, catalytic domain / SH2 domain / Tyrosine-protein kinase ABL, SH2 domain / Protein kinase-like domain superfamily ...Tyrosine-protein kinase, active site / SH3-like domain superfamily / F-actin binding / Protein kinase, ATP binding site / Tyrosine-protein kinase, catalytic domain / Tyrosine-protein kinase ABL1/transforming protein Abl / Serine-threonine/tyrosine-protein kinase, catalytic domain / SH2 domain / Tyrosine-protein kinase ABL, SH2 domain / Protein kinase-like domain superfamily / SH3 domain / Protein kinase domain / SH2 domain superfamily / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
gb:62362414: / Tyrosine-protein kinase ABL1
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å|
|Authors||Young, M.A. / Shah, N.P. / Chao, L.H. / Zarrinkar, P. / Sawyers, P. / Kuriyan, J.|
|Citation||Journal: Cancer Res. / Year: 2006|
Title: Structure of the kinase domain of an imatinib-resistant Abl mutant in complex with the Aurora kinase inhibitor VX-680.
Authors: Young, M.A. / Shah, N.P. / Chao, L.H. / Seeliger, M. / Milanov, Z.V. / Biggs, W.H. / Treiber, D.K. / Patel, H.K. / Zarrinkar, P.P. / Lockhart, D.J. / Sawyers, C.L. / Kuriyan, J.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
A: Proto-oncogene tyrosine-protein kinase ABL1
|#1: Protein|| |
Mass: 33171.938 Da / Num. of mol.: 1 / Fragment: Kinase domain, residues 227-513 / Mutation: H396P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL1, ABL, JTK7 / Plasmid: pET28a-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-star
References: GenBank: 62362414, UniProt: P00519*PLUS, EC: 22.214.171.124
|#2: Chemical|| ChemComp-VX6 / |
|#3: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.65 Å3/Da / Density % sol: 53.67 %|
|Crystal grow||Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 |
Details: 25% w/v PEG1500, 0.1M citric acid, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å|
|Detector||Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 26, 2004|
|Radiation||Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 1 Å / Relative weight: 1|
|Reflection||Resolution: 1.9→50 Å / Num. obs: 24731 / % possible obs: 90.4 % / Rmerge(I) obs: 0.121 / Χ2: 1.036|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: PDB ENTRY 1M52
Resolution: 1.91→44.29 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Cross-validation method: -> "throughout" Free R value test set selection criteria: -> "random"
|Solvent computation||Solvent model: CNS bulk solvent model used / Bsol: 47.7103 Å2 / ksol: 0.391374 e/Å3|
|Displacement parameters||Biso max: 77.63 Å2 / Biso mean: 25.8 Å2 / Biso min: 10.41 Å2|
|Refinement step||Cycle: LAST / Resolution: 1.91→44.29 Å|
|Refine LS restraints|
|LS refinement shell|
Refinement-ID: X-RAY DIFFRACTION
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