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Open data
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Basic information
Entry | Database: PDB / ID: 5mtj | |||||||||
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Title | Yes1-SH2 in complex with monobody Mb(Yes_1) | |||||||||
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![]() | SIGNALING PROTEIN / Monobody / Src homology / Signaling | |||||||||
Function / homology | ![]() PECAM1 interactions / Signaling by ERBB2 / CD28 co-stimulation / CTLA4 inhibitory signaling / Regulation of KIT signaling / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / Signaling by SCF-KIT / regulation of glucose transmembrane transport ...PECAM1 interactions / Signaling by ERBB2 / CD28 co-stimulation / CTLA4 inhibitory signaling / Regulation of KIT signaling / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / Signaling by SCF-KIT / regulation of glucose transmembrane transport / FCGR activation / Regulation of signaling by CBL / epidermal growth factor receptor binding / postsynaptic specialization, intracellular component / cellular response to platelet-derived growth factor stimulus / extrinsic component of cytoplasmic side of plasma membrane / cellular response to retinoic acid / cell surface receptor protein tyrosine kinase signaling pathway / cellular response to transforming growth factor beta stimulus / phosphotyrosine residue binding / phosphorylation / actin filament / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / positive regulation of peptidyl-tyrosine phosphorylation / protein tyrosine kinase activity / transmembrane transporter binding / cell differentiation / innate immune response / signaling receptor binding / centrosome / glutamatergic synapse / Golgi apparatus / enzyme binding / positive regulation of transcription by RNA polymerase II / ATP binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sha, F. / Kukenshoner, T. / Koide, S. / Hantschel, O. | |||||||||
![]() | ![]() Title: Selective Targeting of SH2 Domain-Phosphotyrosine Interactions of Src Family Tyrosine Kinases with Monobodies. Authors: Kukenshoner, T. / Schmit, N.E. / Bouda, E. / Sha, F. / Pojer, F. / Koide, A. / Seeliger, M. / Koide, S. / Hantschel, O. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.5 KB | Display | ![]() |
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PDB format | ![]() | 45.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5mtmC ![]() 5mtnC ![]() 3k2mS ![]() 4tziS S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 13295.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: Q04736, non-specific protein-tyrosine kinase | ||
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#2: Protein | Mass: 10733.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: synthetic / Source: (gene. exp.) ![]() Production host: ![]() ![]() | ||
#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.36 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 10.25 Details: 2M Ammonium sulfate, 0.2M Lithium sulfate, 0.1M CAPS/NaOH pH10.25 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 1.949→50 Å / Num. obs: 27106 / % possible obs: 99.82 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.04 / Rrim(I) all: 0.131 / Net I/σ(I): 24.44 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 16.1 % / Mean I/σ(I) obs: 1.5 / Rpim(I) all: 0.544 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3K2M and 4TZI Resolution: 1.949→43.308 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.949→43.308 Å
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Refine LS restraints |
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LS refinement shell |
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