[English] 日本語
Yorodumi- PDB-1lkl: HUMAN P56-LCK TYROSINE KINASE SH2 DOMAIN IN COMPLEX WITH THE PHOS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lkl | ||||||
---|---|---|---|---|---|---|---|
Title | HUMAN P56-LCK TYROSINE KINASE SH2 DOMAIN IN COMPLEX WITH THE PHOSPHOTYROSYL PEPTIDE AC-PTYR-GLU-GLU-GLY (PYEEG PEPTIDE) | ||||||
Components |
| ||||||
Keywords | COMPLEX (TYROSINE KINASE/PEPTIDE) / COMPLEX (TYROSINE KINASE-PEPTIDE) / COMPLEX (TYROSINE KINASE-PEPTIDE) complex | ||||||
Function / homology | Function and homology information regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / Fc-gamma receptor signaling pathway / CD28 co-stimulation / FLT3 signaling through SRC family kinases / intracellular zinc ion homeostasis / Nef and signal transduction / CD4 receptor binding / Nef Mediated CD4 Down-regulation / positive regulation of heterotypic cell-cell adhesion ...regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / Fc-gamma receptor signaling pathway / CD28 co-stimulation / FLT3 signaling through SRC family kinases / intracellular zinc ion homeostasis / Nef and signal transduction / CD4 receptor binding / Nef Mediated CD4 Down-regulation / positive regulation of heterotypic cell-cell adhesion / Interleukin-2 signaling / CD28 dependent Vav1 pathway / Regulation of KIT signaling / leukocyte migration / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / phospholipase activator activity / CD8 receptor binding / pericentriolar material / positive regulation of T cell receptor signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / hemopoiesis / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / PD-1 signaling / phosphatidylinositol 3-kinase binding / positive regulation of intrinsic apoptotic signaling pathway / T cell receptor binding / peptidyl-tyrosine autophosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / GPVI-mediated activation cascade / release of sequestered calcium ion into cytosol / T cell costimulation / phosphotyrosine residue binding / SH2 domain binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / non-specific protein-tyrosine kinase / B cell receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / platelet activation / : / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of T cell activation / Downstream TCR signaling / PIP3 activates AKT signaling / DAP12 signaling / T cell receptor signaling pathway / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / protein phosphatase binding / intracellular signal transduction / response to xenobiotic stimulus / protein phosphorylation / membrane raft / innate immune response / signaling receptor binding / protein kinase binding / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Tong, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Crystal structures of the human p56lck SH2 domain in complex with two short phosphotyrosyl peptides at 1.0 A and 1.8 A resolution. Authors: Tong, L. / Warren, T.C. / King, J. / Betageri, R. / Rose, J. / Jakes, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lkl.cif.gz | 36.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lkl.ent.gz | 24.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lkl_validation.pdf.gz | 369.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1lkl_full_validation.pdf.gz | 370 KB | Display | |
Data in XML | 1lkl_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 1lkl_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/1lkl ftp://data.pdbj.org/pub/pdb/validation_reports/lk/1lkl | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11872.214 Da / Num. of mol.: 1 / Fragment: SH2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06239 |
---|---|
#2: Protein/peptide | Mass: 602.485 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.15 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 9668 / % possible obs: 98 % / Num. measured all: 34222 / Rmerge(I) obs: 0.043 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→6 Å / σ(F): 2 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |