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Yorodumi- PDB-3dk6: Crystal structure of mutant ABL kinase domain in complex with sma... -
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-Basic information
Entry | Database: PDB / ID: 3dk6 | ||||||
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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 / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / circulatory system development / podocyte apoptotic process / DN4 thymocyte differentiation ...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 / 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 / transitional one stage B cell differentiation / regulation of modification of synaptic structure / Regulation of actin dynamics for phagocytic cup formation / delta-catenin binding / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / 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 / Myogenesis / bubble DNA binding / activated T cell proliferation / regulation of Cdc42 protein signal transduction / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / syntaxin binding / alpha-beta T cell differentiation / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / cell leading edge / B cell proliferation / regulation of microtubule polymerization / positive regulation of osteoblast proliferation / platelet-derived growth factor receptor-beta signaling pathway / negative regulation of cellular senescence / positive regulation of focal adhesion assembly / associative learning / Bergmann glial cell differentiation / neuromuscular process controlling balance / platelet-derived growth factor receptor signaling pathway / negative regulation of BMP signaling pathway / negative regulation of mitotic cell cycle / negative regulation of long-term synaptic potentiation / endothelial cell migration / positive regulation of T cell migration / canonical NF-kappaB signal transduction / signal transduction in response to DNA damage / negative regulation of double-strand break repair via homologous recombination / BMP signaling pathway / phagocytosis / negative regulation of endothelial cell apoptotic process / four-way junction DNA binding / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / spleen development / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / ruffle / positive regulation of establishment of T cell polarity / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / ephrin receptor binding / actin filament polymerization / phosphotyrosine residue binding / response to endoplasmic reticulum stress / positive regulation of mitotic cell cycle / SH2 domain binding / substrate adhesion-dependent cell spreading / positive regulation of release of sequestered calcium ion into cytosol / post-embryonic development / thymus development / neural tube closure / establishment of localization in cell / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / neuron differentiation / epidermal growth factor receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / autophagy / cell-cell adhesion / SH3 domain binding / cellular response to hydrogen peroxide 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 | 3dk6.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dk6.ent.gz | 96 KB | Display | PDB format |
PDBx/mmJSON format | 3dk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dk6_validation.pdf.gz | 970.5 KB | Display | wwPDB validaton report |
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Full document | 3dk6_full_validation.pdf.gz | 973 KB | Display | |
Data in XML | 3dk6_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 3dk6_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/3dk6 ftp://data.pdbj.org/pub/pdb/validation_reports/dk/3dk6 | HTTPS FTP |
-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: 34016.746 Da / Num. of mol.: 2 / Mutation: Y253F, 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: 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: 2.89 Å3/Da / Density % sol: 57.48 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 5.6 Details: 1.95M AMMONIUM SULFATE, 125 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: Feb 9, 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: 2.016→29.847 Å / Num. obs: 52435 / % possible obs: 99.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 4.5 |
-Processing
Software |
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Refinement | Resolution: 2.02→29.8 Å / Occupancy max: 1 / Occupancy min: 1 /
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Displacement parameters | Biso max: 96.61 Å2 / Biso mean: 32.348 Å2 / Biso min: 10.38 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→29.8 Å
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