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Yorodumi- PDB-1qpj: CRYSTAL STRUCTURE OF THE LYMPHOCYTE-SPECIFIC KINASE LCK IN COMPLE... -
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-Basic information
Entry | Database: PDB / ID: 1qpj | |||||||||
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Title | CRYSTAL STRUCTURE OF THE LYMPHOCYTE-SPECIFIC KINASE LCK IN COMPLEX WITH STAUROSPORINE. | |||||||||
Components | LCK TYROSINE KINASE | |||||||||
Keywords | TRANSFERASE / ALPHA BETA FOLD | |||||||||
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 / CD4 receptor binding / FLT3 signaling through SRC family kinases / Nef and signal transduction / Nef Mediated CD4 Down-regulation / Interleukin-2 signaling ...regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / Fc-gamma receptor signaling pathway / CD28 co-stimulation / intracellular zinc ion homeostasis / CD4 receptor binding / FLT3 signaling through SRC family kinases / Nef and signal transduction / Nef Mediated CD4 Down-regulation / Interleukin-2 signaling / CD28 dependent Vav1 pathway / positive regulation of heterotypic cell-cell adhesion / protein serine/threonine phosphatase activity / Regulation of KIT signaling / CTLA4 inhibitory signaling / phospholipase activator activity / leukocyte migration / positive regulation of T cell receptor signaling pathway / pericentriolar material / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / PECAM1 interactions / phospholipase binding / CD28 dependent PI3K/Akt signaling / RHOH GTPase cycle / hemopoiesis / Generation of second messenger molecules / immunological synapse / T cell differentiation / PD-1 signaling / CD8 receptor binding / phosphatidylinositol 3-kinase binding / positive regulation of intrinsic apoptotic signaling pathway / peptidyl-tyrosine autophosphorylation / release of sequestered calcium ion into cytosol / GPVI-mediated activation cascade / T cell costimulation / extrinsic component of cytoplasmic side of plasma membrane / SH2 domain binding / phosphotyrosine residue binding / T cell receptor 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 / cell surface receptor protein tyrosine kinase signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of T cell activation / Downstream TCR signaling / PIP3 activates AKT signaling / DAP12 signaling / ATPase binding / T cell receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein phosphatase binding / protein tyrosine kinase activity / intracellular signal transduction / response to xenobiotic stimulus / membrane raft / signaling receptor binding / protein phosphorylation / innate immune response / 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: 2.2 Å | |||||||||
Authors | Zhu, X. / Kim, J.L. / Rose, P.E. / Stover, D.R. / Toledo, L.M. | |||||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Structural analysis of the lymphocyte-specific kinase Lck in complex with non-selective and Src family selective kinase inhibitors. Authors: Zhu, X. / Kim, J.L. / Newcomb, J.R. / Rose, P.E. / Stover, D.R. / Toledo, L.M. / Zhao, H. / Morgenstern, K.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qpj.cif.gz | 84 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qpj.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/1qpj ftp://data.pdbj.org/pub/pdb/validation_reports/qp/1qpj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32353.818 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: LYMPHOCYTE / Plasmid: PFASTBAC1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P06239, EC: 2.7.1.112 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-STU / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.16 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M TRIS PH 8.5 0.25 M LI2SO4 20% POLYETHYLENE GLYCOL 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 24, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→35 Å / Num. obs: 16145 / % possible obs: 96.4 % / Observed criterion σ(I): -1 / Redundancy: 3.3 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.202 / % possible all: 94.3 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 35 Å / Redundancy: 3.3 % / Num. measured all: 53567 / Biso Wilson estimate: 21.5 Å2 |
Reflection shell | *PLUS % possible obs: 94 % / Redundancy: 3.1 % |
-Processing
Software |
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Refinement | Resolution: 2.2→6 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 98 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.262 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |