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- PDB-1lkk: HUMAN P56-LCK TYROSINE KINASE SH2 DOMAIN IN COMPLEX WITH THE PHOS... -
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Basic information
Entry | Database: PDB / ID: 1lkk | ||||||
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Title | HUMAN P56-LCK TYROSINE KINASE SH2 DOMAIN IN COMPLEX WITH THE PHOSPHOTYROSYL PEPTIDE AC-PTYR-GLU-GLU-ILE (PYEEI PEPTIDE) | ||||||
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![]() | COMPLEX (TYROSINE KINASE/PEPTIDE) / COMPLEX (TYROSINE KINASE-PEPTIDE) / COMPLEX (TYROSINE KINASE-PEPTIDE) complex | ||||||
Function / homology | ![]() 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 / 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 / FLT3 signaling through SRC family kinases / intracellular zinc ion homeostasis / 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 / phospholipase activator activity / leukocyte migration / 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 / T cell receptor binding / peptidyl-tyrosine autophosphorylation / positive regulation of intrinsic apoptotic signaling pathway / release of sequestered calcium ion into cytosol / cell surface receptor protein tyrosine kinase signaling pathway / GPVI-mediated activation cascade / 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 / positive regulation of T cell activation / Downstream TCR signaling / DAP12 signaling / PIP3 activates AKT 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 | ![]() | ||||||
![]() | Tong, L. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 94.3 KB | Display | ![]() |
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PDB format | ![]() | 71.5 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: 11985.371 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 658.591 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-ACE / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.28 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1 Å / Num. obs: 48786 / % possible obs: 91 % / Num. measured all: 170160 / Rmerge(I) obs: 0.07 |
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Processing
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Refinement | Resolution: 1→30 Å / σ(I): -3 Details: THE REFINEMENT WAS CARRIED OUT AGAINST F**2. REFLECTIONS THAT HAVE NEGATIVE INTENSITIES ARE INCLUDED IN THE REFINEMENT. RESIDUES 170 - 176 HAVE WEAK ELECTRON DENSITY. RESIDUES LEU 122, HIS ...Details: THE REFINEMENT WAS CARRIED OUT AGAINST F**2. REFLECTIONS THAT HAVE NEGATIVE INTENSITIES ARE INCLUDED IN THE REFINEMENT. RESIDUES 170 - 176 HAVE WEAK ELECTRON DENSITY. RESIDUES LEU 122, HIS 148, THR 177, ARG 184, AND ARG 196 HAVE WEAK SIDE CHAIN ELECTRON DENSITY. ANISOTROPIC TEMPERATURE FACTORS WERE REFINED FOR ALL NON-HYDROGEN ATOMS. HYDROGEN ATOMS FOR THE SH2 DOMAIN AND THE INHIBITOR WERE INCLUDED IN THE REFINEMENT, WITH RIDING ISOTROPIC TEMPERATURE FACTOR VALUES. HYDROGEN ATOMS ON THE WATER MOLECULES WERE NOT INCLUDED.
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Refinement step | Cycle: LAST / Resolution: 1→30 Å
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Refine LS restraints |
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Refine LS restraints | *PLUS Type: s_angle_deg / Dev ideal: 1.7 |