[English] 日本語
![](img/lk-miru.gif)
- PDB-2ivs: Crystal structure of non-phosphorylated RET tyrosine kinase domain -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2ivs | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of non-phosphorylated RET tyrosine kinase domain | |||||||||
![]() | PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET | |||||||||
![]() | 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 | ![]() 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 | ![]() ![]() ![]() | |||||||||
![]() | Knowles, P.P. / Murray-Rust, J. / McDonald, N.Q. | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 130.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 98.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 511.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 515.6 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ivtC ![]() 2ivuC ![]() 2ivvC ![]() 1gjoS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
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.) ![]() ![]() ![]() References: UniProt: P07949, receptor protein-tyrosine kinase #2: Chemical | ChemComp-FMT / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | 705-1013 CORRESPOND | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 47.7 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|