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- PDB-2oi3: NMR Structure Analysis of the Hematopoetic Cell Kinase SH3 Domain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2oi3 | ||||||
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Title | NMR Structure Analysis of the Hematopoetic Cell Kinase SH3 Domain complexed with an artificial high affinity ligand (PD1) | ||||||
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![]() | TRANSFERASE / human Hck / SH3 / Src-type tyrosine kinase | ||||||
Function / homology | ![]() leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / regulation of podosome assembly / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization ...leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / regulation of podosome assembly / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / mesoderm development / FCGR activation / localization / type II interferon-mediated signaling pathway / Signaling by CSF3 (G-CSF) / lipopolysaccharide-mediated signaling pathway / transport vesicle / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / cell surface receptor protein tyrosine kinase signaling pathway / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / caveola / cell projection / integrin-mediated signaling pathway / Regulation of signaling by CBL / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / regulation of inflammatory response / protein tyrosine kinase activity / protein autophosphorylation / cell differentiation / lysosome / cytoskeleton / cell adhesion / intracellular signal transduction / inflammatory response / protein phosphorylation / intracellular membrane-bounded organelle / innate immune response / focal adhesion / signaling receptor binding / lipid binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / Golgi apparatus / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / Simulated annealing with generalized born solvent model, NMR distance constraints | ||||||
Model type details | minimized average | ||||||
![]() | Schmidt, H. / Stoldt, M. / Hoffmann, S. / Tran, T. / Willbold, D. | ||||||
![]() | ![]() Title: Solution Structure of a Hck SH3 Domain Ligand Complex Reveals Novel Interaction Modes Authors: Schmidt, H. / Hoffmann, S. / Tran, T. / Stoldt, M. / Stangler, T. / Wiesehan, K. / Willbold, D. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.3 KB | Display | ![]() |
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PDB format | ![]() | 29.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 405.8 KB | Display | ![]() |
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Full document | ![]() | 406.5 KB | Display | |
Data in XML | ![]() | 5 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2oj2C C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 9497.373 Da / Num. of mol.: 1 / Fragment: SH3 domain, residues 60-140 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P08631, non-specific protein-tyrosine kinase |
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#2: Protein/peptide | Mass: 1374.649 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 1.3mM Hck-SH3 U-13C, U-15N: 1.3mM PD1, 20mM KPO4, 20mM NaCl, pH 6.7, 93% H2O, 7% D2O Solvent system: 93% H2O/7% D2O |
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Sample conditions | Ionic strength: 20mM KPO4, 20mM NaCl / pH: 6.7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: Simulated annealing with generalized born solvent model, NMR distance constraints Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: Minimized average structure / Conformers calculated total number: 20 / Conformers submitted total number: 1 |