|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
Role of ABL in ROBO-SLIT signaling / Regulation of actin dynamics for phagocytic cup formation / Myogenesis / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / Cyclin D associated events in G1 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / RUNX2 regulates osteoblast differentiation ...Role of ABL in ROBO-SLIT signaling / Regulation of actin dynamics for phagocytic cup formation / Myogenesis / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / Cyclin D associated events in G1 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / RUNX2 regulates osteoblast differentiation / mitochondrial depolarization / transitional one stage B cell differentiation / positive regulation of actin filament binding / activation of protein kinase C activity / DNA conformation change / negative regulation of phospholipase C activity / actin filament branching / positive regulation of interleukin-2 secretion / positive regulation blood vessel branching / nicotinate-nucleotide adenylyltransferase activity / B cell proliferation involved in immune response / positive regulation of microtubule binding / neuroepithelial cell differentiation / positive regulation of Wnt signaling pathway, planar cell polarity pathway / regulation of extracellular matrix organization / microspike assembly / regulation of modification of synaptic structure / cerebellum morphogenesis / collateral sprouting / B-1 B cell homeostasis / cardiovascular system development / positive regulation of oxidoreductase activity / alpha-beta T cell differentiation / activated T cell proliferation / bubble DNA binding / neuropilin signaling pathway / neuropilin binding / regulation of T cell differentiation / regulation of Cdc42 protein signal transduction / negative regulation of protein serine/threonine kinase activity / negative regulation of ubiquitin-protein transferase activity / regulation of microtubule polymerization / regulation of actin cytoskeleton reorganization / negative regulation of BMP signaling pathway / mitogen-activated protein kinase binding / sequence-specific double-stranded DNA binding / proline-rich region binding / positive regulation of interferon-gamma secretion / negative regulation of cell-cell adhesion / cellular response to dopamine / syntaxin binding / regulation of response to DNA damage stimulus / DNA damage induced protein phosphorylation / negative regulation of cellular senescence / positive regulation of osteoblast proliferation / cell leading edge / regulation of axon extension / actin monomer binding / positive regulation of cell migration involved in sprouting angiogenesis / platelet-derived growth factor receptor-beta signaling pathway / negative regulation of long-term synaptic potentiation / neuromuscular process controlling balance / Bergmann glial cell differentiation / positive regulation of focal adhesion assembly / regulation of hematopoietic stem cell differentiation / mismatch repair / positive regulation of muscle cell differentiation / positive regulation of actin cytoskeleton reorganization / regulation of endocytosis / negative regulation of mitotic cell cycle / regulation of cell adhesion / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell motility / negative regulation of endothelial cell apoptotic process / four-way junction DNA binding / endothelial cell migration / positive regulation of stress fiber assembly / regulation of actin cytoskeleton organization / signal transduction in response to DNA damage / substrate adhesion-dependent cell spreading / regulation of autophagy / positive regulation of endothelial cell migration / cellular protein modification process / spleen development / SH2 domain binding / post-embryonic development / neural tube closure / positive regulation of mitotic cell cycle / negative regulation of I-kappaB kinase/NF-kappaB signaling / positive regulation of release of sequestered calcium ion into cytosol / thymus development / protein kinase C binding / negative regulation of ERK1 and ERK2 cascade / phosphotyrosine residue binding / ephrin receptor binding / integrin-mediated signaling pathway / actin cytoskeleton organization / autophagy / non-specific protein-tyrosine kinase / peptidyl-tyrosine autophosphorylation
SH2 domain superfamily / SH2 domain / Protein kinase domain profile. / Src homology 3 (SH3) domain profile. / Src homology 2 (SH2) domain profile. / Tyrosine protein kinases specific active-site signature. / SH2 domain / F-actin binding / Protein tyrosine kinase / SH3 domain ...SH2 domain superfamily / SH2 domain / Protein kinase domain profile. / Src homology 3 (SH3) domain profile. / Src homology 2 (SH2) domain profile. / Tyrosine protein kinases specific active-site signature. / SH2 domain / F-actin binding / Protein tyrosine kinase / SH3 domain / Protein kinase domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / SH3 domain / Tyrosine-protein kinase, active site / Protein kinase-like domain superfamily / F-actin binding / Protein kinase, ATP binding site / Tyrosine-protein kinase, catalytic domain / Tyrosine-protein kinase ABL1/transforming protein Abl / Tyrosine-protein kinase ABL, SH2 domain / SH3-like domain superfamily / Protein kinases ATP-binding region signature.
Tyrosine-protein kinase ABL1 / gb:62362414:
|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/peptide|| |
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: 220.127.116.11
|#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
Refinement-ID: X-RAY DIFFRACTION
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi