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- PDB-6i83: Crystal structure of phosphorylated RET V804M tyrosine kinase dom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i83 | ||||||||||||
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Title | Crystal structure of phosphorylated RET V804M tyrosine kinase domain complexed with PDD00018366 | ||||||||||||
![]() | Proto-oncogene tyrosine-protein kinase receptor Ret | ||||||||||||
![]() | ONCOPROTEIN / inhibitor / kinase / proto-oncogene | ||||||||||||
Function / homology | ![]() Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / posterior midgut development / ureter maturation / embryonic epithelial tube formation / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / membrane protein proteolysis / positive regulation of peptidyl-serine phosphorylation of STAT protein / Formation of the ureteric bud ...Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / posterior midgut development / ureter maturation / embryonic epithelial tube formation / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / membrane protein proteolysis / positive regulation of peptidyl-serine phosphorylation of STAT protein / Formation of the ureteric bud / positive regulation of neuron maturation / Formation of the nephric duct / enteric nervous system development / neuron cell-cell adhesion / innervation / plasma membrane protein complex / neuron maturation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of cell adhesion mediated by integrin / neural crest cell migration / ureteric bud development / response to pain / regulation of axonogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / positive regulation of cell size / RET signaling / regulation of cell adhesion / cellular response to retinoic acid / NPAS4 regulates expression of target genes / transmembrane receptor protein tyrosine kinase activity / axon guidance / receptor protein-tyrosine kinase / positive regulation of neuron projection development / activation of cysteine-type endopeptidase activity involved in apoptotic process / MAPK cascade / retina development in camera-type eye / signaling receptor activity / RAF/MAP kinase cascade / protein tyrosine kinase activity / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / receptor complex / endosome membrane / positive regulation of cell migration / response to xenobiotic stimulus / axon / protein phosphorylation / neuronal cell body / calcium ion binding / dendrite / positive regulation of gene expression / positive regulation of DNA-templated transcription / signal transduction / ATP binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Burschowsky, D. / Seewooruthun, C. / Bayliss, R. / Carr, M.D. / Echalier, A. / Jordan, A.M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery and Optimization of wt-RET/KDR-Selective Inhibitors of RETV804MKinase. Authors: Newton, R. / Waszkowycz, B. / Seewooruthun, C. / Burschowsky, D. / Richards, M. / Hitchin, S. / Begum, H. / Watson, A. / French, E. / Hamilton, N. / Jones, S. / Lin, L.Y. / Waddell, I. / ...Authors: Newton, R. / Waszkowycz, B. / Seewooruthun, C. / Burschowsky, D. / Richards, M. / Hitchin, S. / Begum, H. / Watson, A. / French, E. / Hamilton, N. / Jones, S. / Lin, L.Y. / Waddell, I. / Echalier, A. / Bayliss, R. / Jordan, A.M. / Ogilvie, D. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.7 KB | Display | ![]() |
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PDB format | ![]() | 57 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 768.4 KB | Display | ![]() |
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Full document | ![]() | 769.5 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i82C ![]() 2ivsS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35820.277 Da / Num. of mol.: 1 / Mutation: V804M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P07949, receptor protein-tyrosine kinase | ||
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#2: Chemical | ChemComp-H72 / | ||
#3: Chemical | ChemComp-FMT / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.82 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium citrate pH 4.5-5.5, 2.0 M sodium formate drop size 500 nl + 500 nl RET at 3 mg/ml in 20 mM Tris pH 8.0, 100 mM NaCl, 1 mM DTT PH range: 4.5-5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→49.77 Å / Num. obs: 30797 / % possible obs: 98.8 % / Redundancy: 5.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.159 / Rrim(I) all: 0.175 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 1.88→1.93 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1646 / CC1/2: 0.337 / % possible all: 82.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2IVS Resolution: 1.88→45 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.592 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.135 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.439 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→45 Å
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