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Yorodumi- PDB-6yoj: FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH 6-[4-(3-Me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yoj | ||||||
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Title | FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH 6-[4-(3-Methanesulfonyl-benzylamino)-5-trifluoromethyl-pyrimidin-2-ylamino]-3,4-dihydro-1H-quinolin-2-one | ||||||
Components | Focal adhesion kinase 1 | ||||||
Keywords | TRANSFERASE / PROTEIN TYROSINE KINASE / ATP BINDING / TRANSFERASE-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of macrophage proliferation / positive regulation of fibroblast migration ...netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of macrophage proliferation / positive regulation of fibroblast migration / DCC mediated attractive signaling / Signal regulatory protein family interactions / growth hormone receptor signaling pathway / regulation of osteoblast differentiation / MET activates PTK2 signaling / regulation of focal adhesion assembly / establishment of cell polarity / positive regulation of wound healing / negative regulation of cell-cell adhesion / regulation of GTPase activity / positive regulation of macrophage chemotaxis / Fc-gamma receptor signaling pathway involved in phagocytosis / p130Cas linkage to MAPK signaling for integrins / positive regulation of epithelial cell migration / regulation of cytoskeleton organization / Apoptotic cleavage of cellular proteins / regulation of cell adhesion mediated by integrin / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of anoikis / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / ephrin receptor signaling pathway / positive regulation of protein kinase activity / regulation of cell adhesion / vascular endothelial growth factor receptor signaling pathway / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / stress fiber / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / Integrin signaling / SH2 domain binding / transforming growth factor beta receptor signaling pathway / ciliary basal body / protein tyrosine phosphatase activity / molecular function activator activity / integrin-mediated signaling pathway / cell motility / FCGR3A-mediated phagocytosis / axon guidance / non-specific protein-tyrosine kinase / regulation of protein phosphorylation / non-membrane spanning protein tyrosine kinase activity / placenta development / epidermal growth factor receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / cell migration / integrin binding / actin binding / regulation of cell population proliferation / cell cortex / regulation of cell shape / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / angiogenesis / protein autophosphorylation / dendritic spine / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / positive regulation of cell migration / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / focal adhesion / centrosome / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.361 Å | ||||||
Authors | Musil, D. / Heinrich, T. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2021 Title: Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2. Authors: Berger, B.T. / Amaral, M. / Kokh, D.B. / Nunes-Alves, A. / Musil, D. / Heinrich, T. / Schroder, M. / Neil, R. / Wang, J. / Navratilova, I. / Bomke, J. / Elkins, J.M. / Muller, S. / Frech, M. ...Authors: Berger, B.T. / Amaral, M. / Kokh, D.B. / Nunes-Alves, A. / Musil, D. / Heinrich, T. / Schroder, M. / Neil, R. / Wang, J. / Navratilova, I. / Bomke, J. / Elkins, J.M. / Muller, S. / Frech, M. / Wade, R.C. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yoj.cif.gz | 131.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yoj.ent.gz | 99.8 KB | Display | PDB format |
PDBx/mmJSON format | 6yoj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yoj_validation.pdf.gz | 738.9 KB | Display | wwPDB validaton report |
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Full document | 6yoj_full_validation.pdf.gz | 739.6 KB | Display | |
Data in XML | 6yoj_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 6yoj_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/6yoj ftp://data.pdbj.org/pub/pdb/validation_reports/yo/6yoj | HTTPS FTP |
-Related structure data
Related structure data | 6yq1C 6yr9C 6yt6C 6yvsC 6yvyC 6yxvC 4gu6S 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: 32304.221 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2, FAK, FAK1 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q05397, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-P4N / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 16% PEG 3350, 0.1 M TRIS, pH 8.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.361→45.33 Å / Num. obs: 360917 / % possible obs: 89.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 13.89 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.09 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.361→1.442 Å / Num. unique obs: 2385 / CC1/2: 0.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GU6 Resolution: 1.361→45.33 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.072 / SU Rfree Blow DPI: 0.072 / SU Rfree Cruickshank DPI: 0.067
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Displacement parameters | Biso max: 58.51 Å2 / Biso mean: 16.96 Å2 / Biso min: 5.77 Å2
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Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.361→45.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.361→1.41 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -6.8878 Å / Origin y: -1.0604 Å / Origin z: 16.4463 Å
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Refinement TLS group | Selection details: { A|* } |