+Open data
-Basic information
Entry | Database: PDB / ID: 4ybk | ||||||
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Title | C-Helix-Out Dasatinib Analog Crystallized with c-Src Kinase | ||||||
Components | Proto-oncogene tyrosine-protein kinase Src | ||||||
Keywords | TRANSFERASE / Protein kinase / C-Helix-Out | ||||||
Function / homology | Function and homology information Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / CD28 co-stimulation / CTLA4 inhibitory signaling / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Recycling pathway of L1 / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RAF activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / Downregulation of ERBB4 signaling / EPH-ephrin mediated repulsion of cells / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / Activated NTRK3 signals through PI3K / Downstream signal transduction / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell junction / protein phosphatase binding / protein tyrosine kinase activity / mitochondrial inner membrane / cell differentiation / cytoskeleton / endosome membrane / regulation of cell cycle / cell adhesion / cell cycle / phosphorylation / signaling receptor binding / focal adhesion / innate immune response / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kwarcinski, F.E. / Brandvold, K.B. / Johnson, T.K. / Phadke, S. / Meagher, J.L. / Seeliger, M.A. / Stuckey, J.A. / Soellner, M.B. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Conformation-Selective Analogues of Dasatinib Reveal Insight into Kinase Inhibitor Binding and Selectivity. Authors: Kwarcinski, F.E. / Brandvold, K.R. / Phadke, S. / Beleh, O.M. / Johnson, T.K. / Meagher, J.L. / Seeliger, M.A. / Stuckey, J.A. / Soellner, M.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ybk.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ybk.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ybk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/4ybk ftp://data.pdbj.org/pub/pdb/validation_reports/yb/4ybk | HTTPS FTP |
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-Related structure data
Related structure data | 4ybjC 4yc8C 4dggS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32726.645 Da / Num. of mol.: 1 / Fragment: UNP residues 251-533 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) References: UniProt: P00523, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-4B7 / |
#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: 2.02 Å3/Da / Density % sol: 39.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES, pH 6.5, 16% PEG 3350, 420 mM NaOAc |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 15, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 9990 / % possible obs: 99.8 % / Redundancy: 12.9 % / Biso Wilson estimate: 33.47 Å2 / Rmerge(I) obs: 0.131 / Χ2: 1.081 / Net I/av σ(I): 22.042 / Net I/σ(I): 5.4 / Num. measured all: 128811 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4dgg Resolution: 2.5→39.62 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.8775 / SU R Cruickshank DPI: 0.723 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.849 / SU Rfree Blow DPI: 0.293 / SU Rfree Cruickshank DPI: 0.291
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Displacement parameters | Biso max: 96.68 Å2 / Biso mean: 28.06 Å2 / Biso min: 6.4 Å2
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Refine analyze | Luzzati coordinate error obs: 0.285 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→39.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.74 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 57.4575 Å / Origin y: 66.6163 Å / Origin z: 117.954 Å
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Refinement TLS group | Selection details: { A|* } |