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- PDB-2x2m: 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: 2x2m | ||||||
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Title | Crystal Structure of phosphorylated RET tyrosine kinase domain with inhibitor | ||||||
![]() | PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET | ||||||
![]() | TRANSFERASE / HIRSCHSPRUNG DISEASE / GDNF RECEPTOR / TRANSMEMBRANE / PROTO-ONCOGENE / PHOSPHOPROTEIN / DISEASE MUTATION / PHOSPHOTRANSFERASE / RET / KINASE / MEMBRANE | ||||||
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. / 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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Download
PDBx/mmCIF format | ![]() | 124.6 KB | Display | ![]() |
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PDB format | ![]() | 94.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.9 KB | Display | ![]() |
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Full document | ![]() | 460.4 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 29.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2x2kC ![]() 2x2lC ![]() 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.00142, -1, -0.00251), Vector: |
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Components
#1: Protein | Mass: 35788.215 Da / Num. of mol.: 2 / Fragment: TYROSINE KINASE DOMAIN, RESIDUES 705-1013 Source method: isolated from a genetically manipulated source 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 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.9 % / 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 1.75 M SODIUM FORMATE, 0.1 SODIUM CITRATE PH 5.5, 0.15 M POTASSIUM THIOCYANATE 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: Aug 3, 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: 2.5→18.99 Å / Num. obs: 23524 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 2.21 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 6.6 / % possible all: 93.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2IVT, FLEXIBLE LOOPS REMOVED Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.581 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.508 / ESU R Free: 0.278 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.346 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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