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- PDB-2oj2: 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: 2oj2 | |||||||||
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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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![]() | SIGNALING PROTEIN / TRANSFERASE/INHIBITOR / human Hck / SH3 / Src-type tyrosine kinase / NMR / TRANSFERASE-INHIBITOR COMPLEX | |||||||||
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 / torsion angle dynamics | |||||||||
![]() | Schmidt, H. / Hoffmann, S. / Tran, T. / Stoldt, M. / Stangler, T. / Wiesehan, K. / 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 | ![]() | 590.4 KB | Display | ![]() |
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PDB format | ![]() | 491.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 354.1 KB | Display | ![]() |
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Full document | ![]() | 592.7 KB | Display | |
Data in XML | ![]() | 38.2 KB | Display | |
Data in CIF | ![]() | 59.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2oi3C 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1374.649 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was identified as high affinity ligand of Hck-SH3 from screening a phage displayed peptide libary, acetylated and amidated |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy |
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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 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
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: the structures are based on a total of 2500 NOE-derived distance constraints | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20 |