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- PDB-8bk0: Crystal structure of human Ephrin type-A receptor 2 (EPHA2) Kinas... -
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Basic information
Entry | Database: PDB / ID: 8bk0 | ||||||
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Title | Crystal structure of human Ephrin type-A receptor 2 (EPHA2) Kinase domain in complex with LDN-211904 | ||||||
![]() | Ephrin type-A receptor 2 | ||||||
![]() | TRANSFERASE / EPHA2 / ECK / Typ I Inhibitor | ||||||
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 / 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 / osteoclast differentiation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhubi, R. / Gerninghaus, J. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of human Ephrin type-A receptor 2 (EPHA2) Kinase domain in complex with LDN-211904 Authors: Zhubi, R. / Gerninghaus, J. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.9 KB | Display | ![]() |
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PDB format | ![]() | 51 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 825.5 KB | Display | ![]() |
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Full document | ![]() | 826.2 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bioS S: Starting model for refinement |
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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, receptor protein-tyrosine kinase | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-QJI / ~{ | #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: 37.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG3350, 10% ethylene glycol, 0.1M bis-tris-propane pH 6.5, 0.2M sodium nitrate PH range: 6.5 |
-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 16, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→38.45 Å / Num. obs: 26328 / % possible obs: 90.1 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.7→1.73 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3575 / CC1/2: 0.727 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8BIO Resolution: 1.7→38.48 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.031 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.105 / 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: 21.743 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→38.48 Å
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