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Yorodumi- PDB-1ksw: Structure of Human c-Src Tyrosine Kinase (Thr338Gly Mutant) in Co... -
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-Basic information
Entry | Database: PDB / ID: 1ksw | ||||||
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Title | Structure of Human c-Src Tyrosine Kinase (Thr338Gly Mutant) in Complex with N6-benzyl ADP | ||||||
Components | PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC | ||||||
Keywords | TRANSFERASE / SH3 / SH2 / Kinase / bump hole / bump-hole / chemical genetics / orthogonal substrate / ATP | ||||||
Function / homology | Function and homology information regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly ...regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly / regulation of cell-cell adhesion / positive regulation of dephosphorylation / response to mineralocorticoid / Regulation of commissural axon pathfinding by SLIT and ROBO / ERBB2 signaling pathway / regulation of epithelial cell migration / positive regulation of protein transport / Regulation of gap junction activity / regulation of vascular permeability / entry of bacterium into host cell / BMP receptor binding / positive regulation of lamellipodium morphogenesis / cellular response to progesterone stimulus / positive regulation of integrin activation / Activated NTRK2 signals through FYN / negative regulation of focal adhesion assembly / skeletal muscle cell proliferation / positive regulation of protein processing / negative regulation of telomerase activity / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / CD28 co-stimulation / positive regulation of glucose metabolic process / transcytosis / Activated NTRK3 signals through PI3K / connexin binding / cellular response to fluid shear stress / focal adhesion assembly / signal complex assembly / response to acidic pH / podosome / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / positive regulation of podosome assembly / Regulation of RUNX1 Expression and Activity / regulation of bone resorption / branching involved in mammary gland duct morphogenesis / DCC mediated attractive signaling / negative regulation of mitochondrial depolarization / adherens junction organization / osteoclast development / myoblast proliferation / EPH-Ephrin signaling / Ephrin signaling / odontogenesis / cellular response to peptide hormone stimulus / Signal regulatory protein family interactions / cellular response to fatty acid / MET activates PTK2 signaling / regulation of early endosome to late endosome transport / oogenesis / Receptor Mediated Mitophagy / GP1b-IX-V activation signalling / Regulation of KIT signaling / Signaling by ALK / postsynaptic specialization, intracellular component / CTLA4 inhibitory signaling / Signaling by EGFR / phospholipase activator activity / leukocyte migration / DNA biosynthetic process / EPHA-mediated growth cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / interleukin-6-mediated signaling pathway / p130Cas linkage to MAPK signaling for integrins / negative regulation of hippo signaling / positive regulation of epithelial cell migration / positive regulation of Notch signaling pathway / stress fiber assembly / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / regulation of heart rate by cardiac conduction / Recycling pathway of L1 / RUNX2 regulates osteoblast differentiation / progesterone receptor signaling pathway / dendritic growth cone / stimulatory C-type lectin receptor signaling pathway / negative regulation of telomere maintenance via telomerase / uterus development / PECAM1 interactions / phospholipase binding / neurotrophin TRK receptor signaling pathway / Long-term potentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / FCGR activation / EPH-ephrin mediated repulsion of cells / negative regulation of anoikis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Witucki, L.A. / Huang, X. / Shah, K. / Liu, Y. / Kyin, S. / Eck, M.J. / Shokat, K.M. | ||||||
Citation | Journal: Chem.Biol. / Year: 2002 Title: Mutant tyrosine kinases with unnatural nucleotide specificity retain the structure and phospho-acceptor specificity of the wild-type enzyme. Authors: Witucki, L.A. / Huang, X. / Shah, K. / Liu, Y. / Kyin, S. / Eck, M.J. / Shokat, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ksw.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ksw.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ksw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/1ksw ftp://data.pdbj.org/pub/pdb/validation_reports/ks/1ksw | HTTPS FTP |
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-Related structure data
Related structure data | 2srcS 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: 51665.520 Da / Num. of mol.: 1 / Fragment: SH3, SH2 and Kinase domains / Mutation: T338G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12931, EC: 2.7.1.112 |
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#2: Chemical | ChemComp-NBS / |
#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: 2.29 Å3/Da / Density % sol: 46.29 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% PEG 4000, 50mM PIPES pH 6.5, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.917 Å |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Sep 16, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 12715 / Num. obs: 12715 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.071 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. measured all: 46549 / Rmerge(I) obs: 0.071 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2SRC Resolution: 2.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.231 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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