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- PDB-3lck: THE KINASE DOMAIN OF HUMAN LYMPHOCYTE KINASE (LCK), ACTIVATED FOR... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lck | ||||||
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Title | THE KINASE DOMAIN OF HUMAN LYMPHOCYTE KINASE (LCK), ACTIVATED FORM (AUTO-PHOSPHORYLATED ON TYR394) | ||||||
![]() | PROTO-ONCOGENE TYROSINE-PROTEIN KINASE | ||||||
![]() | TYROSINE-PROTEIN KINASE / ATP-BINDING / PHOSPHORYLATION / SIGNAL TRANSDUCTION | ||||||
Function / homology | ![]() regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / Fc-gamma receptor signaling pathway / CD28 co-stimulation / intracellular zinc ion homeostasis / FLT3 signaling through SRC family kinases / CD4 receptor binding / Nef Mediated CD4 Down-regulation / Nef and signal transduction / 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 / intracellular zinc ion homeostasis / FLT3 signaling through SRC family kinases / CD4 receptor binding / Nef Mediated CD4 Down-regulation / Nef and signal transduction / positive regulation of heterotypic cell-cell adhesion / Interleukin-2 signaling / CD28 dependent Vav1 pathway / Regulation of KIT signaling / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / leukocyte migration / 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 / RHOH GTPase cycle / hemopoiesis / Generation of second messenger molecules / immunological synapse / T cell differentiation / PD-1 signaling / phosphatidylinositol 3-kinase binding / T cell receptor binding / positive regulation of intrinsic apoptotic signaling pathway / peptidyl-tyrosine autophosphorylation / release of sequestered calcium ion into cytosol / extrinsic component of cytoplasmic side of plasma membrane / GPVI-mediated activation cascade / cell surface receptor protein tyrosine kinase signaling pathway / T cell costimulation / phosphotyrosine residue binding / SH2 domain binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / platelet activation / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / activation of cysteine-type endopeptidase activity involved in apoptotic process / Downstream TCR signaling / positive regulation of T cell activation / PIP3 activates AKT signaling / DAP12 signaling / T cell receptor signaling pathway / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein phosphatase binding / protein tyrosine kinase activity / intracellular signal transduction / response to xenobiotic stimulus / membrane raft / protein phosphorylation / innate immune response / signaling receptor binding / protein kinase binding / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() ![]() | ||||||
![]() | Yamaguchi, H. / Hendrickson, W.A. | ||||||
![]() | ![]() Title: Structural basis for activation of human lymphocyte kinase Lck upon tyrosine phosphorylation. Authors: Yamaguchi, H. / Hendrickson, W.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.2 KB | Display | ![]() |
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PDB format | ![]() | 58.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 381.9 KB | Display | ![]() |
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Full document | ![]() | 387.5 KB | Display | |
Data in XML | ![]() | 8.1 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1irkS S: Starting model for refinement |
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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
#1: Protein | Mass: 31425.865 Da / Num. of mol.: 1 / Fragment: PROTEIN TYROSINE KINASE DOMAIN Source method: isolated from a genetically manipulated source Details: PHOSPHORYLATION ON TYR 394 / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.5 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED IN HANGING DROPS WITH 1.6 M AMMONIUM SULFATE AND 0.1 M BISTRIS-HCL (PH 6.5 @ RT) AS A WELL SOLUTION., vapor diffusion - hanging drop Temp details: room temp | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: used to seeding | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jul 21, 1996 / Details: SAGITTAL FOCUSING MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 31599 / % possible obs: 99 % / Redundancy: 8.1 % / Biso Wilson estimate: 13 Å2 / Rsym value: 0.028 / Net I/σ(I): 37 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 21.8 / Rsym value: 0.047 / % possible all: 96.1 |
Reflection | *PLUS Rmerge(I) obs: 0.028 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / % possible obs: 96.1 % / Rmerge(I) obs: 0.047 |
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Processing
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Refinement | Method to determine structure: ![]() ![]() ![]() Starting model: PDB ENTRY 1IRK Resolution: 1.7→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED Cross valid method: R FREE THROUGHOUT EXCEPT FOR THE LAST ROUND σ(F): 2
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Displacement parameters | Biso mean: 10.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.78 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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