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- PDB-5ia2: Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ia2 | ||||||
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Title | Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with compound 66 | ||||||
![]() | Ephrin type-A receptor 2 | ||||||
![]() | TRANSFERASE / TYROSINE-PROTEIN KINASE / RECEPTOR / ATP-BINDING | ||||||
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 / ephrin receptor activity / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / bone remodeling / response to growth factor / tight junction / activation of GTPase activity / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / neural tube development / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / mammary gland epithelial cell proliferation / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / vasculogenesis / regulation of angiogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / negative regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / osteoclast differentiation / cell chemotaxis / skeletal system development / molecular function activator activity / protein localization to plasma membrane / cell motility / positive regulation of protein localization to plasma membrane / receptor protein-tyrosine kinase / neuron differentiation / ruffle membrane / osteoblast differentiation / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / lamellipodium / virus receptor activity / receptor complex / cell adhesion / defense response to Gram-positive bacterium / positive regulation of cell migration / inflammatory response / cadherin binding / focal adhesion / cell surface / ATP binding / plasma membrane 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.4 KB | Display | ![]() |
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PDB format | ![]() | 59.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5i9uC ![]() 5i9vC ![]() 5i9wC ![]() 5i9xC ![]() 5i9yC ![]() 5i9zC ![]() 5ia0C ![]() 5ia1C ![]() 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: Ligand ID L66: compound/ligand 66 EDO from cryo soaking Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P29317, receptor protein-tyrosine kinase | ||
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#2: Chemical | ChemComp-L66 / ![]() Source method: isolated from a genetically manipulated source Formula: C22H19N5O4 Details: Ligand ID L66: compound/ligand 66 EDO from cryo soaking Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Chemical | ![]() Source method: isolated from a genetically manipulated source Formula: C2H6O2 Details: Ligand ID L66: compound/ligand 66 EDO from cryo soaking Source: (gene. exp.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.76 % |
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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 MES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.619→53.758 Å / Num. obs: 33944 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.619→1.624 Å / Rmerge(I) obs: 0.537 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1MQB Resolution: 1.619→53.758 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.619→53.758 Å
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Refine LS restraints |
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LS refinement shell |
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