+Open data
-Basic information
Entry | Database: PDB / ID: 7ote | |||||||||
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Title | Src Kinase Domain in complex with ponatinib | |||||||||
Components | Proto-oncogene tyrosine-protein kinase Src | |||||||||
Keywords | ONCOPROTEIN / ATP Inhibitor / Kinase / ligand binding / Cell signalling | |||||||||
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 / entry of bacterium into host cell / regulation of vascular permeability / 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 / 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 / focal adhesion assembly / response to acidic pH / signal complex assembly / podosome / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / Regulation of RUNX1 Expression and Activity / positive regulation of podosome assembly / regulation of bone resorption / branching involved in mammary gland duct morphogenesis / DCC mediated attractive signaling / adherens junction organization / osteoclast development / myoblast proliferation / EPH-Ephrin signaling / Ephrin signaling / negative regulation of mitochondrial depolarization / 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 / Regulation of KIT signaling / Receptor Mediated Mitophagy / Signaling by ALK / postsynaptic specialization, intracellular component / GP1b-IX-V activation signalling / CTLA4 inhibitory signaling / Signaling by EGFR / leukocyte migration / phospholipase activator activity / DNA biosynthetic process / EPHA-mediated growth cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / interleukin-6-mediated signaling pathway / negative regulation of hippo signaling / p130Cas linkage to MAPK signaling for integrins / positive regulation of epithelial cell migration / positive regulation of Notch signaling pathway / cellular response to platelet-derived growth factor stimulus / stress fiber assembly / positive regulation of smooth muscle cell migration / Recycling pathway of L1 / RUNX2 regulates osteoblast differentiation / regulation of heart rate by cardiac conduction / progesterone receptor signaling pathway / dendritic growth cone / stimulatory C-type lectin receptor signaling pathway / uterus development / PECAM1 interactions / phospholipase binding / neurotrophin TRK receptor signaling pathway / Long-term potentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of telomere maintenance via telomerase / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / negative regulation of anoikis / RET signaling / FCGR activation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å | |||||||||
Authors | Soriano-Maldonado, P. / Cuesta-Hernandez, H.N. / Plaza-Menacho, I. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: An allosteric switch between the activation loop and a c-terminal palindromic phospho-motif controls c-Src function. Authors: Cuesta-Hernandez, H.N. / Contreras, J. / Soriano-Maldonado, P. / Sanchez-Wandelmer, J. / Yeung, W. / Martin-Hurtado, A. / Munoz, I.G. / Kannan, N. / Llimargas, M. / Munoz, J. / Plaza-Menacho, I. #1: Journal: Biorxiv / Year: 2023 Title: Src Kinase Domain in complex with ponatinib Authors: Soriano-Maldonado, p. / Cuesta-Hernandez, H.N. / Plaza-Menacho, I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ote.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ote.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ote.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/7ote ftp://data.pdbj.org/pub/pdb/validation_reports/ot/7ote | HTTPS FTP |
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-Related structure data
Related structure data | 3el8S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 33585.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 6xH corresponds to the purification tag / Source: (gene. exp.) Homo sapiens (human) / Gene: SRC, SRC1 / Production host: Escherichia coli (E. coli) References: UniProt: P12931, non-specific protein-tyrosine kinase #2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.51 Å3/Da / Density % sol: 51.08 % / Description: Thin needles |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Tris 20 mM pH 8, 150 mM Sodium chloride, 1 mM DTT, 2-propanol and PEG 4.000 PH range: 7-8.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2019 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.49→63.59 Å / Num. obs: 21420 / % possible obs: 85.2 % / Redundancy: 2.5 % / CC1/2: 0.924 / Rmerge(I) obs: 0.18 / Rrim(I) all: 0.225 / Net I/σ(I): 5.1 | |||||||||||||||
Reflection shell | Resolution: 2.49→8.94 Å / Rmerge(I) obs: 0.041 / Num. unique obs: 20255 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EL8 Resolution: 2.49→63.59 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.079 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.62 Å2 / Biso mean: 43.689 Å2 / Biso min: 16.59 Å2
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Refinement step | Cycle: final / Resolution: 2.49→63.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.494→2.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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