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Yorodumi- PDB-2ivs: Crystal structure of non-phosphorylated RET tyrosine kinase domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ivs | |||||||||
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Title | Crystal structure of non-phosphorylated RET tyrosine kinase domain | |||||||||
Components | PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET | |||||||||
Keywords | TRANSFERASE / NUCLEOTIDE-BINDING / HIRSCHSPRUNG DISEASE / PHOSPHORYLATION / DISEASE MUTATION / PHOSPHOTRANSFERASE / TYROSINE-PROTEIN KINASE / CHROMOSOMAL TRANSLOCATION / POLYMORPHISM / GDNF RECEPTOR / TRANSMEMBRANE / PROTO-ONCOGENE / TYROSINE KINASE / RET / KINASE / MEMBRANE / ATP-BINDING | |||||||||
Function / homology | Function and homology information GDF15-GFRAL signaling pathway / 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 ...GDF15-GFRAL signaling pathway / 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 / neuron cell-cell adhesion / Formation of the nephric duct / enteric nervous system development / 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 / regulation of axonogenesis / response to pain / homophilic cell adhesion via plasma membrane adhesion molecules / positive regulation of cell size / RET signaling / transmembrane receptor protein tyrosine kinase activity / regulation of cell adhesion / cellular response to retinoic acid / NPAS4 regulates expression of target genes / axon guidance / receptor protein-tyrosine kinase / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron projection development / MAPK cascade / retina development in camera-type eye / signaling receptor activity / RAF/MAP kinase cascade / protein tyrosine kinase activity / receptor complex / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome membrane / early endosome / positive regulation of cell migration / response to xenobiotic stimulus / protein phosphorylation / axon / neuronal cell body / dendrite / calcium ion binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / signal transduction / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Knowles, P.P. / Murray-Rust, J. / McDonald, N.Q. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structure and Chemical Inhibition of the Ret Tyrosine Kinase Domain. Authors: Knowles, P.P. / Murray-Rust, J. / Kjaer, S. / Scott, R.P. / Hanrahan, S. / Santoro, M. / Ibanez, C.F. / McDonald, N.Q. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ivs.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ivs.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ivs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/2ivs ftp://data.pdbj.org/pub/pdb/validation_reports/iv/2ivs | HTTPS FTP |
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-Related structure data
Related structure data | 2ivtC 2ivuC 2ivvC 1gjoS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.10484, -0.98257, 0.15349), Vector: |
-Components
#1: Protein | Mass: 35708.234 Da / Num. of mol.: 2 / Fragment: TYROSINE KINASE DOMAIN, UNP RESIDUES 705-1013 Source method: isolated from a genetically manipulated source Details: 5 N-TERMINAL VECTOR-DERIVED RESIDUES GPLSL / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PBACPAK-HIS3 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: P07949, receptor protein-tyrosine kinase #2: Chemical | ChemComp-FMT / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | 705-1013 CORRESPOND | |
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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: 2.22 Å3/Da / Density % sol: 47.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: PROTEIN 3 MG/ML IN 20 MM TRIS-HCL PH 8.0, 10MM NACL, 1MM DTT RESERVOIR 2.0 M SODIUM FORMATE, 0.1M SODIUM CITRATE PH 5.5 VAPOUR DIFFUSION, SITTING DROP,295 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 8, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2→27.9 Å / Num. obs: 41522 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 10 / % possible all: 80.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GJO Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.64 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.161 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.26 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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