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Yorodumi- PDB-5ia0: Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ia0 | ||||||
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Title | Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with alisertib (MLN8237) | ||||||
Components | Ephrin type-A receptor 2 | ||||||
Keywords | TRANSFERASE / TYROSINE-PROTEIN KINASE / RECEPTOR / ATP-BINDING | ||||||
Function / homology | Function and homology information 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 / post-anal tail morphogenesis / bone remodeling / transmembrane-ephrin receptor activity / 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 / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / vasculogenesis / regulation of angiogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / negative regulation of angiogenesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / osteoclast differentiation / regulation of ERK1 and ERK2 cascade / cell chemotaxis / skeletal system development / molecular function activator activity / protein localization to plasma membrane / cell motility / positive regulation of protein localization to plasma membrane / axon guidance / receptor protein-tyrosine kinase / 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 / cadherin binding / inflammatory response / phosphorylation / focal adhesion / dendrite / cell surface / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.948 Å | ||||||
Authors | Kudlinzki, D. / Linhard, V.L. / Gande, S.L. / Sreeramulu, S. / Saxena, K. / Heinzlmeir, S. / Medard, G. / Kuester, B. / Schwalbe, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ia0.cif.gz | 189.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ia0.ent.gz | 149.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ia0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ia0_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5ia0_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5ia0_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 5ia0_validation.cif.gz | 53.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/5ia0 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/5ia0 | HTTPS FTP |
-Related structure data
Related structure data | 5i9uC 5i9vC 5i9wC 5i9xC 5i9yC 5i9zC 5ia1C 5ia2C 5ia3C 5ia4C 5ia5C 1mqbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 34462.840 Da / Num. of mol.: 3 / Fragment: UNP residues 596-900 Source method: isolated from a genetically manipulated source Details: Ligand ID UNL: unknown ligand alisertib EDO from cryo soaking Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P29317, receptor protein-tyrosine kinase #2: Chemical | #3: Chemical | ChemComp-EDO / Mass: 62.068 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Formula: C2H6O2 Details: Ligand ID UNL: unknown ligand alisertib EDO from cryo soaking Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: receptor protein-tyrosine kinase #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 37.5 % MPD_P1k_P3350, 0.3 M Carboxylic Acids, 0.1 M BufferSystem3 pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 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: 1.948→48.2 Å / Num. obs: 76440 / % possible obs: 99.8 % / Redundancy: 7.41 % / Rpim(I) all: 0.117 / Net I/σ(I): 12.28 |
Reflection shell | Resolution: 1.948→2.07 Å / Rpim(I) all: 1.658 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MQB Resolution: 1.948→46.865 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.73 / 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: 1.948→46.865 Å
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Refine LS restraints |
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LS refinement shell |
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