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Yorodumi- PDB-3oxz: Crystal structure of ABL kinase domain bound with a DFG-out inhib... -
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-Basic information
Entry | Database: PDB / ID: 3oxz | ||||||
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Title | Crystal structure of ABL kinase domain bound with a DFG-out inhibitor AP24534 | ||||||
Components | Tyrosine-protein kinase ABL1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / protein-inhibitor complex / protein kinase two-domain fold / phosphotransferase / ATP binding / phosphorylation / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / transitional one stage B cell differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / circulatory system development / podocyte apoptotic process ...Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / transitional one stage B cell differentiation / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / circulatory system development / podocyte apoptotic process / DN4 thymocyte differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / response to epinephrine / regulation of cellular senescence / regulation of modification of synaptic structure / positive regulation of extracellular matrix organization / delta-catenin binding / B cell proliferation involved in immune response / Regulation of actin dynamics for phagocytic cup formation / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / regulation of extracellular matrix organization / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / Myogenesis / regulation of Cdc42 protein signal transduction / activated T cell proliferation / regulation of axon extension / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / alpha-beta T cell differentiation / syntaxin binding / cardiac muscle cell proliferation / regulation of T cell differentiation / negative regulation of double-strand break repair via homologous recombination / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / regulation of microtubule polymerization / B cell proliferation / positive regulation of osteoblast proliferation / cell leading edge / platelet-derived growth factor receptor-beta signaling pathway / positive regulation of focal adhesion assembly / negative regulation of cellular senescence / negative regulation of long-term synaptic potentiation / Bergmann glial cell differentiation / associative learning / neuromuscular process controlling balance / platelet-derived growth factor receptor signaling pathway / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / endothelial cell migration / positive regulation of T cell migration / canonical NF-kappaB signal transduction / BMP signaling pathway / phagocytosis / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / four-way junction DNA binding / signal transduction in response to DNA damage / positive regulation of vasoconstriction / spleen development / positive regulation of stress fiber assembly / ruffle / ERK1 and ERK2 cascade / cellular response to transforming growth factor beta stimulus / positive regulation of establishment of T cell polarity / positive regulation of interleukin-2 production / actin filament polymerization / SH2 domain binding / response to endoplasmic reticulum stress / phosphotyrosine residue binding / ephrin receptor binding / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / post-embryonic development / protein kinase C binding / positive regulation of release of sequestered calcium ion into cytosol / positive regulation of endothelial cell migration / thymus development / neural tube closure / integrin-mediated signaling pathway / establishment of localization in cell / regulation of actin cytoskeleton organization / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / cell-cell adhesion / neuron differentiation / cellular response to hydrogen peroxide / autophagy Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Zhou, T. / Huang, W.S. / Wang, Y. / Thomas, M. / Keats, J. / Xu, Q. / Rivera, V. / Shakespeare, W.C. / Clackson, T. / Dalgarno, D.C. / Zhu, X. | ||||||
Citation | Journal: Chem.Biol.Drug Des. / Year: 2011 Title: Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib (AP24534): Lessons for Overcoming Kinase Inhibitor Resistance. Authors: Zhou, T. / Commodore, L. / Huang, W.S. / Wang, Y. / Thomas, M. / Keats, J. / Xu, Q. / Rivera, V.M. / Shakespeare, W.C. / Clackson, T. / Dalgarno, D.C. / Zhu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oxz.cif.gz | 70.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oxz.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 3oxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/3oxz ftp://data.pdbj.org/pub/pdb/validation_reports/ox/3oxz | HTTPS FTP |
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-Related structure data
Related structure data | 3oy3C 1iepS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32797.438 Da / Num. of mol.: 1 / Fragment: UNP residues 229-511 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abl1, Abl / Production host: Escherichia coli (E. coli) References: UniProt: P00520, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-0LI / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% w/v polyethylene glycol, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 28, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 16703 / Num. obs: 15384 / % possible obs: 92.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 89.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IEP Resolution: 2.2→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 66.56 Å2 / Biso mean: 34.1192 Å2 / Biso min: 17.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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Xplor file |
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