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- PDB-7r8x: Crystal Structure of the LNK SH2 Domain in Complex with an EPOR p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r8x | ||||||
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Title | Crystal Structure of the LNK SH2 Domain in Complex with an EPOR pY454 Phosphopeptide | ||||||
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![]() | SIGNALING PROTEIN / LNK / SH2B3 / JAK/STAT / MPNs | ||||||
Function / homology | ![]() negative regulation of Kit signaling pathway / monocyte homeostasis / thrombopoietin-mediated signaling pathway / stem cell factor receptor binding / Regulation of KIT signaling / Negative regulation of FLT3 / negative regulation of sprouting angiogenesis / negative regulation of chemokine-mediated signaling pathway / negative regulation of response to cytokine stimulus / negative regulation of tyrosine phosphorylation of STAT protein ...negative regulation of Kit signaling pathway / monocyte homeostasis / thrombopoietin-mediated signaling pathway / stem cell factor receptor binding / Regulation of KIT signaling / Negative regulation of FLT3 / negative regulation of sprouting angiogenesis / negative regulation of chemokine-mediated signaling pathway / negative regulation of response to cytokine stimulus / negative regulation of tyrosine phosphorylation of STAT protein / regulation of regulatory T cell differentiation / Factors involved in megakaryocyte development and platelet production / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of platelet aggregation / neutrophil homeostasis / cellular response to chemokine / transmembrane receptor protein tyrosine kinase adaptor activity / cellular response to interleukin-3 / embryonic hemopoiesis / megakaryocyte development / phosphate ion binding / hemopoiesis / hematopoietic stem cell differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / erythrocyte development / protein tyrosine kinase binding / negative regulation of MAP kinase activity / signaling receptor complex adaptor activity / intracellular signal transduction / negative regulation of cell population proliferation / protein-containing complex binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morris, R. / Kershaw, N.J. / Babon, J.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional analysis of target recognition by the lymphocyte adaptor protein LNK. Authors: Morris, R. / Zhang, Y. / Ellyard, J.I. / Vinuesa, C.G. / Murphy, J.M. / Laktyushin, A. / Kershaw, N.J. / Babon, J.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.7 KB | Display | ![]() |
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PDB format | ![]() | 24.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.9 KB | Display | ![]() |
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Full document | ![]() | 424 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 8.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r8wC ![]() 2hdvS C: citing same article ( 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: 12682.654 Da / Num. of mol.: 1 / Fragment: UNP residues 328-438 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1065.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.57 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 20% PEG8000, 0.05 M magnesium acetate, 0.1 M Tris, ph 8.5 |
-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: Jun 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95374 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→33.9 Å / Num. obs: 7318 / % possible obs: 99.78 % / Redundancy: 9.6 % / Biso Wilson estimate: 53.5 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04408 / Rpim(I) all: 0.01481 / Rrim(I) all: 0.04655 / Net I/σ(I): 31 |
Reflection shell | Resolution: 2.301→2.383 Å / Rmerge(I) obs: 0.4924 / Mean I/σ(I) obs: 2.81 / Num. unique obs: 724 / CC1/2: 0.904 / CC star: 0.974 / Rrim(I) all: 0.539 / % possible all: 99.45 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2HDV Resolution: 2.3→33.9 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.29 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.72 Å2 / Biso mean: 53.8189 Å2 / Biso min: 30.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→33.9 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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