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- PDB-1nuk: CRYSTAL STRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE EPHB2 RECEP... -
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Basic information
Entry | Database: PDB / ID: 1nuk | ||||||
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Title | CRYSTAL STRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE EPHB2 RECEPTOR TYROSINE KINASE | ||||||
![]() | PROTEIN (TYROSINE-PROTEIN KINASE RECEPTOR EPH) | ||||||
![]() | TRANSFERASE / EPH RECEPTOR TYROSINE KINASE | ||||||
Function / homology | ![]() regulation of T-helper 17 type immune response / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / Ephrin signaling / negative regulation of NMDA glutamate receptor activity / EPH-Ephrin signaling / hindbrain tangential cell migration / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / positive regulation of NMDA glutamate receptor activity ...regulation of T-helper 17 type immune response / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / Ephrin signaling / negative regulation of NMDA glutamate receptor activity / EPH-Ephrin signaling / hindbrain tangential cell migration / vesicle-mediated intercellular transport / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / positive regulation of NMDA glutamate receptor activity / regulation of body fluid levels / urogenital system development / optic nerve morphogenesis / tight junction assembly / postsynaptic membrane assembly / neuron projection retraction / ephrin receptor activity / axon guidance receptor activity / central nervous system projection neuron axonogenesis / negative regulation of axonogenesis / positive regulation of long-term neuronal synaptic plasticity / regulation of autophagosome assembly / positive regulation of dendritic spine morphogenesis / dendritic spine development / positive regulation of synaptic plasticity / corpus callosum development / regulation of filopodium assembly / camera-type eye morphogenesis / regulation of behavioral fear response / transmembrane-ephrin receptor activity / commissural neuron axon guidance / positive regulation of protein localization to cell surface / negative regulation of cell adhesion / dendritic spine morphogenesis / negative regulation of Ras protein signal transduction / axonal fasciculation / positive regulation of synapse assembly / regulation of receptor signaling pathway via JAK-STAT / positive regulation of immunoglobulin production / regulation of synapse assembly / inner ear morphogenesis / regulation of axonogenesis / retinal ganglion cell axon guidance / B cell activation / roof of mouth development / regulation of neuronal synaptic plasticity / regulation of blood coagulation / negative regulation of cytokine production involved in inflammatory response / ephrin receptor signaling pathway / positive regulation of B cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / hippocampal mossy fiber to CA3 synapse / axonogenesis / negative regulation of protein phosphorylation / learning / positive regulation of long-term synaptic potentiation / positive regulation of protein localization to plasma membrane / animal organ morphogenesis / axon guidance / negative regulation of protein kinase activity / cell morphogenesis / receptor protein-tyrosine kinase / negative regulation of ERK1 and ERK2 cascade / peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production / presynaptic membrane / signaling receptor activity / amyloid-beta binding / postsynapse / cellular response to lipopolysaccharide / postsynaptic membrane / protein tyrosine kinase activity / angiogenesis / dendritic spine / learning or memory / positive regulation of cell migration / phosphorylation / axon / signaling receptor binding / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / positive regulation of gene expression / cell surface / nucleoplasm / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Himanen, J.-P. / Henkemeyer, M. / Nikolov, D.B. | ||||||
![]() | ![]() Title: Crystal structure of the ligand-binding domain of the receptor tyrosine kinase EphB2. Authors: Himanen, J.P. / Henkemeyer, M. / Nikolov, D.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 44.8 KB | Display | ![]() |
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PDB format | ![]() | 32.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 366.8 KB | Display | ![]() |
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Full document | ![]() | 376 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 21139.881 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.94 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.0 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→8 Å / Num. obs: 4214 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 |
Reflection | *PLUS Redundancy: 5 % |
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Processing
Software | Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 24.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→8 Å
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Refine LS restraints |
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Software | *PLUS Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 7.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.9 Å2 |