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Yorodumi- PDB-1lcj: SH2 (SRC HOMOLOGY-2) DOMAIN OF HUMAN P56-LCK TYROSINE KINASE COMP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lcj | ||||||
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Title | SH2 (SRC HOMOLOGY-2) DOMAIN OF HUMAN P56-LCK TYROSINE KINASE COMPLEXED WITH THE 11 RESIDUE PHOSPHOTYROSYL PEPTIDE EPQPYEEIPIYL | ||||||
Components |
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Keywords | COMPLEX (KINASE/PEPTIDE) / COMPLEX (KINASE-PEPTIDE) / COMPLEX (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 / 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 / host cell membrane / 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 / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Eck, M. / Harrison, S. | ||||||
Citation | Journal: Nature / Year: 1993 Title: Recognition of a high-affinity phosphotyrosyl peptide by the Src homology-2 domain of p56lck. Authors: Eck, M.J. / Shoelson, S.E. / Harrison, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lcj.cif.gz | 36.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lcj.ent.gz | 24.9 KB | Display | PDB format |
PDBx/mmJSON format | 1lcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lcj_validation.pdf.gz | 376.3 KB | Display | wwPDB validaton report |
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Full document | 1lcj_full_validation.pdf.gz | 377 KB | Display | |
Data in XML | 1lcj_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 1lcj_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/1lcj ftp://data.pdbj.org/pub/pdb/validation_reports/lc/1lcj | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: GLU A 123 - PRO A 124 OMEGA = 114.65 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Protein | Mass: 12388.826 Da / Num. of mol.: 1 / Mutation: INS(MET 118) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P06239, EC: 2.7.1.112 |
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#2: Protein/peptide | Mass: 1473.515 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source References: UniProt: P03079 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.95 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 4.6 | |||||||||||||||||||||||||||||||||||
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: 1.8 Å / Num. obs: 9956 / Num. measured all: 47097 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 2.2 Å / % possible obs: 85 % |
-Processing
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Refinement | Rfactor Rwork: 0.208 / Rfactor obs: 0.208 / Highest resolution: 1.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refine LS restraints |
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