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- PDB-3ad4: Crystal Structure of Methoxy Benzofuran Derivative bound to the K... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ad4 | ||||||
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Title | Crystal Structure of Methoxy Benzofuran Derivative bound to the Kinase domain of human LCK, (auto-phosphorylated on TYR394) | ||||||
![]() | Proto-oncogene tyrosine-protein kinase LCK | ||||||
![]() | TRANSFERASE / TYROSINE-PROTEIN KINASE / ATP-BINDING / PHOSPHORYLATION / SIGNAL TRANSDUCTION / KINASE / SH2 DOMAIN / SH3 DOMAIN | ||||||
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 / 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 / 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 / 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 | ![]() ![]() ![]() | ||||||
![]() | Tsuji, E. | ||||||
![]() | ![]() Title: Ab initio fragment molecular orbital study of ligand binding to leukocyte-specific protein tyrosine (LCK) kinase Authors: Ozawa, M. / Ozawa, T. / Tsuji, E. / Okazaki, K. / Takeda, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.1 KB | Display | ![]() |
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PDB format | ![]() | 54.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 704.6 KB | Display | ![]() |
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Full document | ![]() | 705.1 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ac1C ![]() 3ac2C ![]() 3ac3C ![]() 3ac4C ![]() 3ac8C ![]() 3acjC ![]() 3ackC ![]() 3ad5C ![]() 3ad6C ![]() 3lckS S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33065.602 Da / Num. of mol.: 1 / Fragment: RESIDUES 225-509 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P06239, non-specific protein-tyrosine kinase |
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-Non-polymers , 5 types, 196 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/KBM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/KBM.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-DMS / | #4: Chemical | ChemComp-MPD / ( | #5: Chemical | ChemComp-KBM / ( | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.65 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M (NH4)2SO4, 0.1M SODIUM CACODYLATE, 30% PEG 8000, 0.2% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 1, 2002 |
Radiation | Monochromator: Si 111 CHANNEL / 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→28.5 Å / Num. all: 14486 / Num. obs: 14511 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.124 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 7.3 / Num. unique all: 2007 / Rsym value: 0.245 / % possible all: 92.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3LCK Resolution: 2.2→10 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.842 / SU B: 5.979 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.349 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.559 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.254 Å / Total num. of bins used: 20
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