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Yorodumi- PDB-4z16: Crystal Structure of the Jak3 Kinase Domain Covalently Bound to N... -
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-Basic information
Entry | Database: PDB / ID: 4z16 | ||||||
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Title | Crystal Structure of the Jak3 Kinase Domain Covalently Bound to N-(3-(((5-chloro-2-((2-methoxy-4-(4-methylpiperazin-1-yl)phenyl)amino)pyrimidin-4-yl)amino)methyl)phenyl)acrylamide | ||||||
Components | Tyrosine-protein kinase JAK3 | ||||||
Keywords | Transferase/Transferase Inhibitor / tyrosine kinase / kinase domain / covalent inhibitor complex / transferase / Transferase-Transferase Inhibitor complex | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | McNally, R. / Tan, L. / Gray, N.S. / Eck, M.J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Development of Selective Covalent Janus Kinase 3 Inhibitors. Authors: Tan, L. / Akahane, K. / McNally, R. / Reyskens, K.M. / Ficarro, S.B. / Liu, S. / Herter-Sprie, G.S. / Koyama, S. / Pattison, M.J. / Labella, K. / Johannessen, L. / Akbay, E.A. / Wong, K.K. / ...Authors: Tan, L. / Akahane, K. / McNally, R. / Reyskens, K.M. / Ficarro, S.B. / Liu, S. / Herter-Sprie, G.S. / Koyama, S. / Pattison, M.J. / Labella, K. / Johannessen, L. / Akbay, E.A. / Wong, K.K. / Frank, D.A. / Marto, J.A. / Look, T.A. / Arthur, J.S. / Eck, M.J. / Gray, N.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z16.cif.gz | 466.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z16.ent.gz | 383.9 KB | Display | PDB format |
PDBx/mmJSON format | 4z16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z16_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 4z16_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 4z16_validation.xml.gz | 42.3 KB | Display | |
Data in CIF | 4z16_validation.cif.gz | 53.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/4z16 ftp://data.pdbj.org/pub/pdb/validation_reports/z1/4z16 | HTTPS FTP |
-Related structure data
Related structure data | 1yvjS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35960.840 Da / Num. of mol.: 4 / Fragment: UNP residues 811-1124 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: JAK3 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P52333, non-specific protein-tyrosine kinase #2: Chemical | ChemComp-4LH / #3: Water | ChemComp-HOH / | Sequence details | QS to PE conflict in UNP entry P52333 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-tris pH 6.5, 16% PEG 3350, 0.2 M ammonium sulfate, 5 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→92.91 Å / Num. obs: 30357 / % possible obs: 97 % / Redundancy: 2.2 % / Biso Wilson estimate: 64.79 Å2 / Rsym value: 0.13 / Net I/σ(I): 7.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YVJ Resolution: 2.9→92.91 Å / Cor.coef. Fo:Fc: 0.8894 / Cor.coef. Fo:Fc free: 0.8563 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.365
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Displacement parameters | Biso mean: 65.05 Å2
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Refine analyze | Luzzati coordinate error obs: 0.423 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.9→92.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å / Total num. of bins used: 15
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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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