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Yorodumi- PDB-3dk3: Crystal structure of mutant ABL kinase domain in complex with sma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dk3 | ||||||
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Title | Crystal structure of mutant ABL kinase domain in complex with small molecule fragment | ||||||
Components | Proto-oncogene tyrosine-protein kinase ABL1 | ||||||
Keywords | TRANSFERASE / DRUG DISCOVERY / ABL KINASE / FRAGMENT BASED / Alternative splicing / ATP-binding / Cell adhesion / Chromosomal rearrangement / Cytoplasm / Cytoskeleton / Kinase / Lipoprotein / Magnesium / Manganese / Metal-binding / Myristate / Nucleotide-binding / Nucleus / Phosphoprotein / Proto-oncogene / SH2 domain / SH3 domain | ||||||
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 / Resolution: 2.02 Å | ||||||
Authors | Lewis, H.A. | ||||||
Citation | Journal: To be Published Title: Crystal structure of mutant ABL kinase domain in complex with small molecule fragment Authors: Bounaud, P.-Y. / Gosberg, A. / Hendle, J. / Lewis, H.A. / Romero, R. / Wilson, M.E. / Zhang, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dk3.cif.gz | 125.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dk3.ent.gz | 96.9 KB | Display | PDB format |
PDBx/mmJSON format | 3dk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/3dk3 ftp://data.pdbj.org/pub/pdb/validation_reports/dk/3dk3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33936.766 Da / Num. of mol.: 2 / Mutation: Y393F, L445P 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 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.59 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 5.6 Details: 1.9M AMMONIUM SULFATE, 150 mM POTASSIUM SODIUM TARTRATE, 100 Mm SODIUM CITRATE, pH 5.6, VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97969 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 4, 2007 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97969 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→28.433 Å / Num. obs: 52186 / % possible obs: 99.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.244 / Net I/σ(I): 2.7 |
-Processing
Software |
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Refinement | Resolution: 2.02→28.4 Å / Occupancy max: 1 / Occupancy min: 0.35 /
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Displacement parameters | Biso max: 83.81 Å2 / Biso mean: 23.363 Å2 / Biso min: 5.33 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→28.4 Å
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