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Yorodumi- PDB-2jkm: Focal Adhesion Kinase catalytic domain in complex with bis-anilin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jkm | ||||||
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Title | Focal Adhesion Kinase catalytic domain in complex with bis-anilino pyrimidine inhibitor | ||||||
Components | FOCAL ADHESION KINASE 1PTK2 | ||||||
Keywords | TRANSFERASE / TYROSINE-PROTEIN KINASE / TYROSINE- PROTEIN KINASE / KINASE / MEMBRANE / ATP-BINDING / INTEGRIN SIGNALING / NUCLEOTIDE-BINDING / FOCAL ADHESION / CELL MIGRATION / KINASE INHIBITOR / CELL JUNCTION / CELL MEMBRANE / PHOSPHOPROTEIN | ||||||
Function / homology | Function and homology information Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Integrin signaling ...Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / 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 / angiogenesis involved in wound healing / signal complex assembly / response to pH / negative regulation of cell-substrate adhesion / wound healing, spreading of cells / positive regulation of focal adhesion assembly / negative regulation of anoikis / positive regulation of protein tyrosine kinase activity / regulation of cell adhesion / response to muscle stretch / ciliary basal body / molecular function activator activity / actin filament organization / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / sarcolemma / integrin binding / positive regulation of protein binding / cell cortex / protein tyrosine kinase activity / angiogenesis / protease binding / dendritic spine / protein autophosphorylation / positive regulation of cell migration / focal adhesion / centrosome / positive regulation of cell population proliferation / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Lietha, D. / Eck, M.J. | ||||||
Citation | Journal: Plos One / Year: 2008 Title: Crystal Structures of the Fak Kinase in Complex with Tae226 and Related Bis-Anilino Pyrimidine Inhibitors Reveal a Helical Dfg Conformation. Authors: Lietha, D. / Eck, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jkm.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jkm.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 2jkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/2jkm ftp://data.pdbj.org/pub/pdb/validation_reports/jk/2jkm | HTTPS FTP |
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-Related structure data
Related structure data | 2jkkC 2jkoC 2jkqC 1mp8S C: citing same article (ref.) 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: 31776.801 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 411-686 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PACG2T / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) References: UniProt: Q00944, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-BII / |
#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: 2.08 Å3/Da / Density % sol: 40.78 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 25% PEG4000, 0.1 M TRIS PH8.5, 10 MM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 3, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 10867 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.3→2.37 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.36 / % possible all: 70.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MP8 Resolution: 2.31→37.56 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.888 / SU B: 20.069 / SU ML: 0.258 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.593 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.907 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→37.56 Å
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