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- PDB-7r8w: Crystal Structure of the LNK SH2 Domain in Complex with a JAK2 pY... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r8w | ||||||
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Title | Crystal Structure of the LNK SH2 Domain in Complex with a JAK2 pY813 Phosphopeptide | ||||||
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Function / homology | ![]() negative regulation of Kit signaling pathway / monocyte homeostasis / thrombopoietin-mediated signaling pathway / ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 38.9 KB | Display | ![]() |
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PDB format | ![]() | 23.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7r8xC ![]() 2hdxS 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: 12953.989 Da / Num. of mol.: 1 / Fragment: UNP residues 325-437 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 717.701 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: 1.87 Å3/Da / Density % sol: 34.37 % |
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Crystal grow![]() | Temperature: 281.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium chloride, 20% PEG3350 |
-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: Nov 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→39.59 Å / Num. obs: 8093 / % possible obs: 99.62 % / Redundancy: 3.4 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03577 / Rpim(I) all: 0.02259 / Rrim(I) all: 0.04243 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.84 / Num. unique obs: 798 / CC1/2: 0.863 / Rpim(I) all: 0.2479 / Rrim(I) all: 0.4651 / % possible all: 98.88 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 2HDX Resolution: 1.9→38.59 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.94 / 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: 81.51 Å2 / Biso mean: 38.6619 Å2 / Biso min: 18.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→38.59 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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