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Yorodumi- PDB-6hes: Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hes | ||||||
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Title | Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712 derivative AT050 | ||||||
Components | Ephrin type-A receptor 2 | ||||||
Keywords | TRANSFERASE / Inhibitor / Complex / Protein Tyrosine Kinase | ||||||
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 / 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 / transmembrane receptor protein tyrosine kinase activity / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / negative regulation of angiogenesis / keratinocyte differentiation / RAC1 GTPase cycle / positive regulation of protein localization to plasma membrane / osteoclast differentiation / cell chemotaxis / skeletal system development / molecular function activator activity / protein localization to plasma membrane / cell motility / receptor protein-tyrosine kinase / ruffle membrane / neuron differentiation / osteoblast differentiation / intrinsic apoptotic signaling pathway in response to DNA damage / virus receptor activity / cell migration / lamellipodium / receptor complex / cell adhesion / positive regulation of cell migration / defense response to Gram-positive bacterium / cadherin binding / inflammatory response / focal adhesion / cell surface / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.128 Å | ||||||
Authors | Kudlinzki, D. / Troester, A. / Witt, K. / Linhard, V.L. / Gande, S.L. / Saxena, K. / Schwalbe, H. | ||||||
Citation | Journal: To Be Published Title: Effects of NVP-BHG712 chemical modifications on EPHA2 binding and affinity Authors: Troester, A. / Kudlinzki, D. / Saxena, K. / Gande, S. / Schwalbe, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hes.cif.gz | 134.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hes.ent.gz | 103.9 KB | Display | PDB format |
PDBx/mmJSON format | 6hes.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/6hes ftp://data.pdbj.org/pub/pdb/validation_reports/he/6hes | HTTPS FTP |
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-Related structure data
Related structure data | 6hetC 6heuC 6hevC 6hewC 6hexC 6heyC 6q7bC 6q7cC 6q7dC 6q7eC 6q7fC 6q7gC 6fnfS 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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1 |
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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.) Homo sapiens (human) / Gene: EPHA2, ECK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29317 |
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#2: Chemical | ChemComp-G0H / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.03 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 37.5 % MPD/PEG1000/PEG3350 (MD), 0.1 M Amino Acids Mix (MD), 0.1 M Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 1.128→38.23 Å / Num. obs: 93065 / % possible obs: 95.4 % / Redundancy: 6.47 % / Biso Wilson estimate: 15.2 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.154 / Net I/σ(I): 8.04 |
Reflection shell | Resolution: 1.128→1.2 Å / Redundancy: 4.92 % / Mean I/σ(I) obs: 0.56 / Num. unique obs: 12730 / CC1/2: 0.193 / % possible all: 81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FNF Resolution: 1.128→38.23 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.79 / 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: 1.128→38.23 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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