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- PDB-1ksw: Structure of Human c-Src Tyrosine Kinase (Thr338Gly Mutant) in Co... -
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Open data
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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 | ||||||
![]() | PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC | ||||||
![]() | TRANSFERASE / SH3 / SH2 / Kinase / bump hole / bump-hole / chemical genetics / orthogonal substrate / ATP | ||||||
Function / homology | ![]() 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 / response to mineralocorticoid / positive regulation of dephosphorylation / Regulation of commissural axon pathfinding by SLIT and ROBO / ERBB2 signaling pathway / regulation of epithelial cell migration / entry of bacterium into host cell / positive regulation of protein transport / Regulation of gap junction activity / BMP receptor binding / positive regulation of lamellipodium morphogenesis / cellular response to progesterone stimulus / regulation of vascular permeability / Activated NTRK2 signals through FYN / positive regulation of integrin activation / negative regulation of focal adhesion assembly / positive regulation of protein processing / skeletal muscle cell proliferation / : / intestinal epithelial cell development / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / CD28 co-stimulation / positive regulation of glucose metabolic process / transcytosis / Activated NTRK3 signals through PI3K / connexin binding / cellular response to fluid shear stress / response to acidic pH / focal adhesion assembly / signal complex assembly / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / podosome / regulation of bone resorption / positive regulation of podosome assembly / Regulation of RUNX1 Expression and Activity / branching involved in mammary gland duct morphogenesis / adherens junction organization / DCC mediated attractive signaling / myoblast proliferation / EPH-Ephrin signaling / odontogenesis / negative regulation of mitochondrial depolarization / Ephrin signaling / cellular response to peptide hormone stimulus / osteoclast development / Signal regulatory protein family interactions / cellular response to fatty acid / MET activates PTK2 signaling / regulation of early endosome to late endosome transport / Regulation of KIT signaling / Signaling by ALK / postsynaptic specialization, intracellular component / Receptor Mediated Mitophagy / CTLA4 inhibitory signaling / GP1b-IX-V activation signalling / oogenesis / interleukin-6-mediated signaling pathway / leukocyte migration / phospholipase activator activity / DNA biosynthetic process / Fc-gamma receptor signaling pathway involved in phagocytosis / negative regulation of hippo signaling / EPHA-mediated growth cone collapse / p130Cas linkage to MAPK signaling for integrins / positive regulation of Notch signaling pathway / Signaling by EGFR / cellular response to platelet-derived growth factor stimulus / stress fiber assembly / positive regulation of epithelial cell migration / positive regulation of smooth muscle cell migration / progesterone receptor signaling pathway / RUNX2 regulates osteoblast differentiation / regulation of heart rate by cardiac conduction / Recycling pathway of L1 / dendritic growth cone / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / uterus development / phospholipase binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Long-term potentiation / neurotrophin TRK receptor signaling pathway / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / negative regulation of telomere maintenance via telomerase / negative regulation of anoikis / RET signaling / FCGR activation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Witucki, L.A. / Huang, X. / Shah, K. / Liu, Y. / Kyin, S. / Eck, M.J. / Shokat, K.M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107 KB | Display | ![]() |
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PDB format | ![]() | 79.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 761 KB | Display | ![]() |
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Full document | ![]() | 780.2 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2srcS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NBS / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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: ![]() | ||||||||||||||||||||||||||||||
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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