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- PDB-3lxl: Structural and Thermodynamic Characterization of the TYK2 and JAK... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lxl | ||||||
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Title | Structural and Thermodynamic Characterization of the TYK2 and JAK3 Kinase Domains in Complex with CP-690550 and CMP-6 | ||||||
![]() | Tyrosine-protein kinase JAK3 | ||||||
![]() | TRANSFERASE / TYK2 / JAK3 / inflammation / cancer / PAN Inhibitor / ATP-binding / Disease mutation / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / SCID / SH2 domain / Tyrosine-protein kinase | ||||||
Function / homology | ![]() negative regulation of dendritic cell cytokine production / negative regulation of FasL production / response to interleukin-9 / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 / negative regulation of T-helper 1 cell differentiation / negative regulation of T cell activation / Interleukin-9 signaling / Interleukin-21 signaling ...negative regulation of dendritic cell cytokine production / negative regulation of FasL production / response to interleukin-9 / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 / negative regulation of T-helper 1 cell differentiation / negative regulation of T cell activation / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / interleukin-2-mediated signaling pathway / regulation of T cell apoptotic process / negative regulation of interleukin-12 production / interleukin-15-mediated signaling pathway / tyrosine phosphorylation of STAT protein / negative regulation of thymocyte apoptotic process / Interleukin-15 signaling / Interleukin-2 signaling / regulation of receptor signaling pathway via JAK-STAT / growth hormone receptor binding / Signaling by ALK / extrinsic component of plasma membrane / Interleukin-20 family signaling / negative regulation of interleukin-10 production / enzyme-linked receptor protein signaling pathway / T cell homeostasis / cell surface receptor signaling pathway via JAK-STAT / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / extrinsic component of cytoplasmic side of plasma membrane / Interleukin-7 signaling / B cell differentiation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / RAF/MAP kinase cascade / regulation of apoptotic process / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / Potential therapeutics for SARS / cell differentiation / cytoskeleton / intracellular signal transduction / endosome / protein phosphorylation / innate immune response / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chrencik, J.E. / Benson, T.E. | ||||||
![]() | ![]() Title: Structural and thermodynamic characterization of the TYK2 and JAK3 kinase domains in complex with CP-690550 and CMP-6. Authors: Chrencik, J.E. / Patny, A. / Leung, I.K. / Korniski, B. / Emmons, T.L. / Hall, T. / Weinberg, R.A. / Gormley, J.A. / Williams, J.M. / Day, J.E. / Hirsch, J.L. / Kiefer, J.R. / Leone, J.W. / ...Authors: Chrencik, J.E. / Patny, A. / Leung, I.K. / Korniski, B. / Emmons, T.L. / Hall, T. / Weinberg, R.A. / Gormley, J.A. / Williams, J.M. / Day, J.E. / Hirsch, J.L. / Kiefer, J.R. / Leone, J.W. / Fischer, H.D. / Sommers, C.D. / Huang, H.C. / Jacobsen, E.J. / Tenbrink, R.E. / Tomasselli, A.G. / Benson, T.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.4 KB | Display | ![]() |
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PDB format | ![]() | 55.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 758.4 KB | Display | ![]() |
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Full document | ![]() | 761.6 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lxkC ![]() 3lxnC ![]() 3lxpC ![]() 1yvjS C: citing same article ( 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: 37193.406 Da / Num. of mol.: 1 / Fragment: Kinase Domain / Mutation: C1048S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P52333, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-IZA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG-3350, 0.2 M Ammonium Sulfate, 0.02% phenylurea, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2009 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→25.13 Å / Num. obs: 31422 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rsym value: 0.03 / Net I/σ(I): 47.9 |
Reflection shell | Resolution: 1.74→1.8 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.56 / Rsym value: 0.33 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1YVJ Resolution: 1.74→25.13 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.146 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.115 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.427 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→25.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.785 Å / Total num. of bins used: 20
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