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Open data
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Basic information
Entry | Database: PDB / ID: 5i9u | ||||||
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Title | Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase | ||||||
![]() | 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 | ![]() ![]() ![]() | ||||||
![]() | Kudlinzki, D. / Linhard, V.L. / Gande, S.L. / Sreeramulu, S. / Saxena, K. / Heinzlmeir, S. / Medard, G. / Kuester, B. / Schwalbe, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Chemical Proteomics and Structural Biology Define EPHA2 Inhibition by Clinical Kinase Drugs. Authors: Heinzlmeir, S. / Kudlinzki, D. / Sreeramulu, S. / Klaeger, S. / Gande, S.L. / Linhard, V. / Wilhelm, M. / Qiao, H. / Helm, D. / Ruprecht, B. / Saxena, K. / Medard, G. / Schwalbe, H. / Kuster, B. #1: Journal: Chembiochem / Year: 2016 Title: Expression and Purification of EPHA2 Tyrosine Kinase Domain for Crystallographic and NMR Studies. Authors: Gande, S.L. / Saxena, K. / Sreeramulu, S. / Linhard, V. / Kudlinzki, D. / Heinzlmeir, S. / Reichert, A.J. / Skerra, A. / Kuster, B. / Schwalbe, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.5 KB | Display | ![]() |
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PDB format | ![]() | 56.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5i9vC ![]() 5i9wC ![]() 5i9xC ![]() 5i9yC ![]() 5i9zC ![]() 5ia0C ![]() 5ia1C ![]() 5ia2C ![]() 5ia3C ![]() 5ia4C ![]() 5ia5C ![]() 1mqbS 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: 34462.840 Da / Num. of mol.: 1 / Fragment: UNP residues 596-900 Source method: isolated from a genetically manipulated source Details: EDO from cryo soaking / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P29317, ![]() |
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#2: Chemical | ChemComp-EDO / ![]() ![]() Source method: isolated from a genetically manipulated source Formula: C2H6O2 / Details: EDO from cryo soaking / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.6 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 37.5 % MPD_P1k_P3350, 0.1 M Amino Acids, 0.1 M Bicine/Trizma base pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.88→39.59 Å / Num. obs: 20489 / % possible obs: 94.4 % / Redundancy: 2.22 % / Rpim(I) all: 0.134 / Net I/σ(I): 7.46 |
Reflection shell | Resolution: 1.88→1.99 Å / Rpim(I) all: 0.603 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1MQB Resolution: 1.889→27.712 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.889→27.712 Å
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Refine LS restraints |
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LS refinement shell |
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