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- PDB-2hle: Structural and biophysical characterization of the EPHB4-EPHRINB2... -
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Basic information
Entry | Database: PDB / ID: 2hle | ||||||
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Title | Structural and biophysical characterization of the EPHB4-EPHRINB2 protein protein interaction and receptor specificity. | ||||||
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![]() | TRANSFERASE/TRANSFERASE RECEPTOR / Protein-protein interaction / Receptor tryosine kinase / Bi-directional cell signaling / TRANSFERASE-TRANSFERASE RECEPTOR COMPLEX / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D | ||||||
Function / homology | ![]() venous blood vessel morphogenesis / nephric duct morphogenesis / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / lymph vessel development / ephrin receptor activity / regulation of chemotaxis / regulation of postsynaptic neurotransmitter receptor internalization / cell migration involved in sprouting angiogenesis / adherens junction organization ...venous blood vessel morphogenesis / nephric duct morphogenesis / positive regulation of aorta morphogenesis / positive regulation of cardiac muscle cell differentiation / lymph vessel development / ephrin receptor activity / regulation of chemotaxis / regulation of postsynaptic neurotransmitter receptor internalization / cell migration involved in sprouting angiogenesis / adherens junction organization / EPH-Ephrin signaling / blood vessel morphogenesis / Ephrin signaling / regulation of postsynaptic membrane neurotransmitter receptor levels / keratinocyte proliferation / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / ephrin receptor signaling pathway / negative regulation of keratinocyte proliferation / heart morphogenesis / T cell costimulation / EPHB-mediated forward signaling / ephrin receptor binding / transmembrane receptor protein tyrosine kinase activity / axon guidance / adherens junction / animal organ morphogenesis / postsynaptic density membrane / Schaffer collateral - CA1 synapse / receptor protein-tyrosine kinase / negative regulation of neuron projection development / cell-cell signaling / virus receptor activity / presynaptic membrane / angiogenesis / protein autophosphorylation / receptor complex / cell adhesion / focal adhesion / glutamatergic synapse / positive regulation of cell population proliferation / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chrencik, J.E. / Brooun, A. / Kuhn, P. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) | ||||||
![]() | ![]() Title: Structural and Biophysical Characterization of the EphB4-EphrinB2 Protein-Protein Interaction and Receptor Specificity. Authors: Chrencik, J.E. / Brooun, A. / Kraus, M.L. / Recht, M.I. / Kolatkar, A.R. / Han, G.W. / Seifert, J.M. / Widmer, H. / Auer, M. / Kuhn, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.5 KB | Display | ![]() |
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PDB format | ![]() | 59 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1kgyS S: Starting model for refinement |
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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: 21354.230 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P54760, receptor protein-tyrosine kinase |
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#2: Protein | Mass: 15787.061 Da / Num. of mol.: 1 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 2.2 M Ammonium sulfate, 100 mM Tris, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 1, 2005 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→20 Å / Num. obs: 19785 / % possible obs: 99.63 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.05→2.103 Å / % possible all: 99.93 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KGY Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.902 / SU B: 16.808 / SU ML: 0.225 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.245 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES 74, 96-99 IN B MOLECULE WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS.
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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: 45.738 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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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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