+Open data
-Basic information
Entry | Database: PDB / ID: 4gvj | ||||||
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Title | Tyk2 (JH1) in complex with adenosine di-phosphate | ||||||
Components | Non-receptor tyrosine-protein kinase TYK2 | ||||||
Keywords | HYDROLASE / 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: 2.03 Å | ||||||
Authors | Liang, J. / Abbema, A.V. / Bao, L. / Barrett, K. / Beresini, M. / Berezhkovskiy, L. / Blair, W. / Chang, C. / Driscoll, J. / Eigenbrot, C. ...Liang, J. / Abbema, A.V. / Bao, L. / Barrett, K. / Beresini, M. / Berezhkovskiy, L. / Blair, W. / Chang, C. / Driscoll, J. / Eigenbrot, C. / Ghilardi, N. / Gibbons, P. / Halladay, J. / Johnson, A. / Kohli, P.B. / Lai, Y. / Liimatta, M. / Mantik, P. / Menghrajani, K. / Murray, J. / Sambrone, A. / Shao, Y. / Shia, S. / Shin, Y. / Smith, J. / Sohn, S. / Stanley, M. / Tsui, V. / Ultsch, M. / Wu, L. / Zhang, B. / Magnuson, S. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2013 Title: Lead identification of novel and selective TYK2 inhibitors. Authors: Liang, J. / Tsui, V. / Van Abbema, A. / Bao, L. / Barrett, K. / Beresini, M. / Berezhkovskiy, L. / Blair, W.S. / Chang, C. / Driscoll, J. / Eigenbrot, C. / Ghilardi, N. / Gibbons, P. / ...Authors: Liang, J. / Tsui, V. / Van Abbema, A. / Bao, L. / Barrett, K. / Beresini, M. / Berezhkovskiy, L. / Blair, W.S. / Chang, C. / Driscoll, J. / Eigenbrot, C. / Ghilardi, N. / Gibbons, P. / Halladay, J. / Johnson, A. / Kohli, P.B. / Lai, Y. / Liimatta, M. / Mantik, P. / Menghrajani, K. / Murray, J. / Sambrone, A. / Xiao, Y. / Shia, S. / Shin, Y. / Smith, J. / Sohn, S. / Stanley, M. / Ultsch, M. / Zhang, B. / Wu, L.C. / Magnuson, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gvj.cif.gz | 137.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gvj.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 4gvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gvj_validation.pdf.gz | 749.3 KB | Display | wwPDB validaton report |
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Full document | 4gvj_full_validation.pdf.gz | 751.4 KB | Display | |
Data in XML | 4gvj_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 4gvj_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/4gvj ftp://data.pdbj.org/pub/pdb/validation_reports/gv/4gvj | HTTPS FTP |
-Related structure data
Related structure data | 4gfmC 4gfoC 4gihC 4gmyC 3nz0S 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: 34749.723 Da / Num. of mol.: 1 / Fragment: Kinase domain, UNP residues 885-1176 / Mutation: C936A, Q969A, E971A, K972A, C1142A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TYK2 / Cell line (production host): Tni / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P29597, non-specific protein-tyrosine kinase | ||
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#2: Chemical | ChemComp-ADP / | ||
#3: Chemical | #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: 2.04 Å3/Da / Density % sol: 39.65 % |
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Crystal grow | Temperature: 291 K / pH: 6.5 Details: 20-30% w/v PEG 3350, 0.2M Mg sulfate, 0.1M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2011 / Details: MIRRORS- BERYLLIUM LENSES |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. obs: 19030 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 36.44 Å2 / Rsym value: 0.69 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 2.03→2.1 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.581 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NZ0 Resolution: 2.03→34.93 Å / Cor.coef. Fo:Fc: 0.9494 / Cor.coef. Fo:Fc free: 0.9342 / SU R Cruickshank DPI: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 46.56 Å2
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Refine analyze | Luzzati coordinate error obs: 0.274 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→34.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.14 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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