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Yorodumi- PDB-2ijm: Crystal Structure of Focal Adhesion Kinase Domain with 2 molecule... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ijm | ||||||
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Title | Crystal Structure of Focal Adhesion Kinase Domain with 2 molecules in the Asymmetric Unit Complexed with ADP and ATP | ||||||
Components | Focal Adhesion Kinase 1 | ||||||
Keywords | SIGNALING PROTEIN / TRANSFERASE / kinase catalytic domain | ||||||
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 / Resolution: 2.187 Å | ||||||
Authors | Lee, C.C. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Focal Adhesion Kinase Catalytic Domain Complexed with ATP and Novel 7H-Pyrrolo [2,3-d] pyrimidine Inhibitor Scaffolds Authors: Andersen, C.B. / Ng, K. / Ficarro, S. / Vu, C. / Choi, H.-S. / He, Y. / Spraggon, G. / Gray, N. / Lee, C.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ijm.cif.gz | 122.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ijm.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ijm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ijm_validation.pdf.gz | 521.2 KB | Display | wwPDB validaton report |
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Full document | 2ijm_full_validation.pdf.gz | 529.8 KB | Display | |
Data in XML | 2ijm_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 2ijm_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/2ijm ftp://data.pdbj.org/pub/pdb/validation_reports/ij/2ijm | HTTPS FTP |
-Related structure data
Related structure data | 1jbaS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32231.170 Da / Num. of mol.: 2 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2, FAK, FAK1 / Production host: Escherichia coli (E. coli) References: UniProt: Q05397, non-specific protein-tyrosine kinase #2: Chemical | ChemComp-ATP / | #3: Chemical | ChemComp-ADP / | #4: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 46.89 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% (v/v) PEG-600, 10% glycerol, 0.1M HEPES pH 7.5, 0.05M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 10, 2003 / Details: CURVED SI (111) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.187→34.3 Å / Num. all: 29887 / Num. obs: 28426 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.045 / Rsym value: 0.056 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.187→2.27 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2144 / Rsym value: 0.283 / % possible all: 70.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JBA Resolution: 2.187→34.3 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.895 / SU B: 6.484 / SU ML: 0.169 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 34.932 Å2
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Refinement step | Cycle: LAST / Resolution: 2.187→34.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.187→2.244 Å / Total num. of bins used: 20
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