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Yorodumi- PDB-2oj2: NMR Structure Analysis of the Hematopoetic Cell Kinase SH3 Domain... -
+Open data
-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) | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / TRANSFERASE/INHIBITOR / human Hck / SH3 / Src-type tyrosine kinase / NMR / TRANSFERASE-INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information 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 / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / cell projection / caveola / 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 / cell surface receptor protein tyrosine kinase signaling pathway / 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 / signaling receptor binding / focal adhesion / intracellular membrane-bounded organelle / innate immune response / 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 | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / torsion angle dynamics | |||||||||
Authors | Schmidt, H. / Hoffmann, S. / Tran, T. / Stoldt, M. / Stangler, T. / Wiesehan, K. / Willbold, D. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oj2.cif.gz | 590.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oj2.ent.gz | 491.7 KB | Display | PDB format |
PDBx/mmJSON format | 2oj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/2oj2 ftp://data.pdbj.org/pub/pdb/validation_reports/oj/2oj2 | HTTPS FTP |
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-Related structure data
Related structure data | 2oi3C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: HCK / Plasmid: pGEX6P2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08631, EC: 2.7.1.112 |
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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 |
-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 |