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Yorodumi- PDB-2g2f: A Src-like Inactive Conformation in the Abl Tyrosine Kinase Domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g2f | ||||||
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Title | A Src-like Inactive Conformation in the Abl Tyrosine Kinase Domain | ||||||
Components |
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Keywords | TRANSFERASE / protein kinase | ||||||
Function / homology | Function and homology information positive regulation of actin filament binding / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / activation of protein kinase C activity / DN4 thymocyte differentiation / response to epinephrine / podocyte apoptotic process / transitional one stage B cell differentiation / DNA conformation change ...positive regulation of actin filament binding / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / activation of protein kinase C activity / DN4 thymocyte differentiation / response to epinephrine / podocyte apoptotic process / transitional one stage B cell differentiation / DNA conformation change / Role of ABL in ROBO-SLIT signaling / nicotinate-nucleotide adenylyltransferase activity / regulation of modification of synaptic structure / positive regulation of microtubule binding / delta-catenin binding / positive regulation of extracellular matrix organization / B cell proliferation involved in immune response / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / negative regulation of ubiquitin-protein transferase activity / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / mitochondrial depolarization / negative regulation of protein serine/threonine kinase activity / activated T cell proliferation / cellular response to dopamine / regulation of hematopoietic stem cell differentiation / regulation of cell motility / proline-rich region binding / regulation of Cdc42 protein signal transduction / mitogen-activated protein kinase binding / positive regulation of dendrite development / myoblast proliferation / syntaxin binding / alpha-beta T cell differentiation / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / Fc-gamma receptor signaling pathway involved in phagocytosis / HDR through Single Strand Annealing (SSA) / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / Myogenesis / positive regulation of osteoblast proliferation / regulation of microtubule polymerization / RUNX2 regulates osteoblast differentiation / 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 / regulation of endocytosis / neuromuscular process controlling balance / negative regulation of mitotic cell cycle / negative regulation of long-term synaptic potentiation / actin monomer binding / negative regulation of BMP signaling pathway / negative regulation of double-strand break repair via homologous recombination / endothelial cell migration / signal transduction in response to DNA damage / positive regulation of T cell migration / RHO GTPases Activate WASPs and WAVEs / mismatch repair / regulation of cell adhesion / BMP signaling pathway / negative regulation of endothelial cell apoptotic process / canonical NF-kappaB signal transduction / peptidyl-tyrosine autophosphorylation / positive regulation of substrate adhesion-dependent cell spreading / four-way junction DNA binding / spleen development / positive regulation of vasoconstriction / cellular response to transforming growth factor beta stimulus / positive regulation of stress fiber assembly / ruffle / response to endoplasmic reticulum stress / positive regulation of establishment of T cell polarity / phosphotyrosine residue binding / ephrin receptor binding / positive regulation of interleukin-2 production / ERK1 and ERK2 cascade / actin filament polymerization / SH2 domain binding / positive regulation of endothelial cell migration / post-embryonic development / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading / thymus development / positive regulation of release of sequestered calcium ion into cytosol / integrin-mediated signaling pathway / regulation of autophagy / establishment of localization in cell / neural tube closure / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Levinson, N.M. / Kuchment, O. | ||||||
Citation | Journal: Plos Biol. / Year: 2006 Title: A SRC-like inactive conformation in the abl tyrosine kinase domain. Authors: Levinson, N.M. / Kuchment, O. / Shen, K. / Young, M.A. / Koldobskiy, M. / Karplus, M. / Cole, P.A. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g2f.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g2f.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 2g2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g2f_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2g2f_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2g2f_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 2g2f_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/2g2f ftp://data.pdbj.org/pub/pdb/validation_reports/g2/2g2f | HTTPS FTP |
-Related structure data
Related structure data | 2g1tC 2g2hC 2g2iC 1m52S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33181.957 Da / Num. of mol.: 2 / Fragment: Abl Kinase Domain / Mutation: H396P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABL1, ABL, JTK7 / Production host: Escherichia coli (E. coli) / References: UniProt: P00519 #2: Protein/peptide | | Mass: 1194.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase peptide synthesis #3: Chemical | ChemComp-AGS / | #4: Chemical | ChemComp-112 / | #5: 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: 2.95 Å3/Da / Density % sol: 58.28 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M Bis-Tris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.115879 Å |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115879 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 22582 / Num. obs: 22582 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.11 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.05 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1M52 Resolution: 2.7→50 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 52.8 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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