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Yorodumi- PDB-3lxn: Structural and Thermodynamic Characterization of the TYK2 and JAK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lxn | ||||||
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Title | Structural and Thermodynamic Characterization of the TYK2 and JAK3 Kinase Domains in Complex with CP-690550 and CMP-6 | ||||||
Components | Non-receptor tyrosine-protein kinase TYK2 | ||||||
Keywords | TRANSFERASE / TYK2 / JAK3 / inflammation / cancer / PAN Inhibitor / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / SH2 domain / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information type III interferon-mediated signaling pathway / interleukin-12 receptor complex / interleukin-23 receptor complex / Interleukin-23 signaling / type 1 angiotensin receptor binding / positive regulation of T-helper 17 type immune response / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / Interleukin-12 signaling / Interleukin-27 signaling ...type III interferon-mediated signaling pathway / interleukin-12 receptor complex / interleukin-23 receptor complex / Interleukin-23 signaling / type 1 angiotensin receptor binding / positive regulation of T-helper 17 type immune response / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / Interleukin-12 signaling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-35 Signalling / positive regulation of natural killer cell proliferation / growth hormone receptor binding / Other interleukin signaling / extrinsic component of plasma membrane / Interleukin-20 family signaling / type I interferon-mediated signaling pathway / Interleukin-6 signaling / MAPK3 (ERK1) activation / positive regulation of interleukin-17 production / Interleukin-10 signaling / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling / growth hormone receptor signaling pathway via JAK-STAT / type II interferon-mediated signaling pathway / positive regulation of T cell proliferation / Signaling by CSF3 (G-CSF) / non-specific protein-tyrosine kinase / positive regulation of receptor signaling pathway via JAK-STAT / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / cytoplasmic side of plasma membrane / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of protein localization to nucleus / Interferon alpha/beta signaling / positive regulation of type II interferon production / Signaling by ALK fusions and activated point mutants / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / cell differentiation / cytoskeleton / intracellular signal transduction / immune response / protein phosphorylation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular exosome / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Chrencik, J.E. / Benson, T.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lxn.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lxn.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 3lxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lxn_validation.pdf.gz | 731.9 KB | Display | wwPDB validaton report |
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Full document | 3lxn_full_validation.pdf.gz | 734.9 KB | Display | |
Data in XML | 3lxn_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 3lxn_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/3lxn ftp://data.pdbj.org/pub/pdb/validation_reports/lx/3lxn | HTTPS FTP |
-Related structure data
Related structure data | 3lxkC 3lxlC 3lxpC 1yvjS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 36534.570 Da / Num. of mol.: 1 / Fragment: Kinase Domain / Mutation: C936A, Q969A, E971A, K972A, C1142A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TYK2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 References: UniProt: P29597, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-MI1 / |
#3: 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: 1.96 Å3/Da / Density % sol: 37.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% Ethanol, 0.1 M Tris, 0.3 M magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.5418 Å |
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: 2.5→18.6 Å / Num. all: 10002 / Num. obs: 10002 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rsym value: 0.068 / Net I/σ(I): 31.87 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.102 / Rsym value: 0.19 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1YVJ Resolution: 2.5→18.58 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.881 / SU B: 9.604 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 1.118 / ESU R Free: 0.353 / 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: 15.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→18.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.561 Å / Total num. of bins used: 20
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