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- PDB-8bin: Crystal structure of human Ephrin type-A receptor 2 (EPHA2) Kinas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bin | ||||||
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Title | Crystal structure of human Ephrin type-A receptor 2 (EPHA2) Kinase domain in complex with MR21 | ||||||
![]() | Ephrin type-A receptor 2 | ||||||
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Function / homology | ![]() notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration ...notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / leading edge membrane / negative regulation of chemokine production / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhubi, R. / Rak, M. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Shifting the selectivity of pyrido[2,3-d]pyrimidin-7(8H)-one inhibitors towards the salt-inducible kinase (SIK) subfamily. Authors: Rak, M. / Tesch, R. / Berger, L.M. / Shevchenko, E. / Raab, M. / Tjaden, A. / Zhubi, R. / Balourdas, D.I. / Joerger, A.C. / Poso, A. / Kramer, A. / Elson, L. / Lucic, A. / Kronenberger, T. / ...Authors: Rak, M. / Tesch, R. / Berger, L.M. / Shevchenko, E. / Raab, M. / Tjaden, A. / Zhubi, R. / Balourdas, D.I. / Joerger, A.C. / Poso, A. / Kramer, A. / Elson, L. / Lucic, A. / Kronenberger, T. / Hanke, T. / Strebhardt, K. / Sanhaji, M. / Knapp, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.3 KB | Display | ![]() |
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PDB format | ![]() | 97.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8bioC ![]() 8bziC ![]() 5nkiS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 34462.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P29317, ![]() | ||||||
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#2: Chemical | ChemComp-EDO / ![]() #3: Chemical | ChemComp-QRR / | #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.59 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG3350, 10% ethylene glycol, 0.2M potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.5→38.49 Å / Num. obs: 35835 / % possible obs: 84.2 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 726 / CC1/2: 0.825 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5NKI Resolution: 1.5→38.49 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.449 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.072 / 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: 17.938 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→38.49 Å
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Refine LS restraints |
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