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- PDB-2x2k: Crystal Structure of phosphorylated RET tyrosine kinase domain wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2x2k | ||||||
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Title | Crystal Structure of phosphorylated RET tyrosine kinase domain with inhibitor | ||||||
![]() | PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET | ||||||
![]() | TRANSFERASE / TYROSINE KINASE / HIRSCHSPRUNG DISEASE / TYROSINE-PROTEIN KINASE / PROTO-ONCOGENE / PHOSPHOPROTEIN / PHOSPHOTRANSFERASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Knowles, P.P. / Murray-Rust, J. / Kjaer, S. / McDonald, N.Q. | ||||||
![]() | ![]() Title: Synthesis, structure-activity relationship and crystallographic studies of 3-substituted indolin-2-one RET inhibitors. Authors: Mologni, L. / Rostagno, R. / Brussolo, S. / Knowles, P.P. / Kjaer, S. / Murray-Rust, J. / Rosso, E. / Zambon, A. / Scapozza, L. / McDonald, N.Q. / Lucchini, V. / Gambacorti-Passerini, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 74.1 KB | Display | ![]() |
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PDB format | ![]() | 52.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2x2lC ![]() 2x2mC ![]() 2ivtS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35788.215 Da / Num. of mol.: 1 / Fragment: TYROSINE KINASE DOMAIN, RESIDUES 705-1013 Source method: isolated from a genetically manipulated source Details: RESIDUES 705-1013,5 N-TERMINAL VECTOR-DERIVED RESIDUES GPLSL Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P07949, receptor protein-tyrosine kinase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-X2K / ( | #4: Water | ChemComp-HOH / | Sequence details | 705-1013 CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.7 % / Description: NONE |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: PROTEIN 4.5 MG/ML IN 20 MM TRIS-HCL PH 8, 100MM NACL,1MM DTT, 1MM EDTA RESERVOIR 1.85 M SODIUM FORMATE, 0.1 SODIUM CITRATE PH 5.5, 0.2M LITHIUM CHLORIDE VAPOUR DIFFUSION, SITTING DROP, 289 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 29, 2007 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→21.64 Å / Num. obs: 11886 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2IVT, FLEXIBLE LOOPS REMOVED Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.884 / SU B: 10.037 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.524 / ESU R Free: 0.306 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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