+Open data
-Basic information
Entry | Database: PDB / ID: 7n8t | |||||||||
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Title | Crystal Structure of AMP-bound Human JNK2 | |||||||||
Components | Mitogen-activated protein kinase 9 | |||||||||
Keywords | TRANSFERASE / JNK2 / Mitogen-activated protein kinase 9 / AMP | |||||||||
Function / homology | Function and homology information protein localization to tricellular tight junction / JUN kinase activity / inflammatory response to wounding / positive regulation of macrophage derived foam cell differentiation / positive regulation of cytokine production involved in inflammatory response / positive regulation of podosome assembly / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / mitogen-activated protein kinase / JNK cascade ...protein localization to tricellular tight junction / JUN kinase activity / inflammatory response to wounding / positive regulation of macrophage derived foam cell differentiation / positive regulation of cytokine production involved in inflammatory response / positive regulation of podosome assembly / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / mitogen-activated protein kinase / JNK cascade / cellular response to cadmium ion / protein serine/threonine/tyrosine kinase activity / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of protein ubiquitination / apoptotic signaling pathway / positive regulation of apoptotic signaling pathway / FCERI mediated MAPK activation / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / regulation of circadian rhythm / cellular response to reactive oxygen species / cellular senescence / Signaling by ALK fusions and activated point mutants / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | |||||||||
Authors | Li, L. / Gurbani, D. / Westover, K.D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Med.Chem. / Year: 2023 Title: Development of a Covalent Inhibitor of c-Jun N-Terminal Protein Kinase (JNK) 2/3 with Selectivity over JNK1. Authors: Lu, W. / Liu, Y. / Gao, Y. / Geng, Q. / Gurbani, D. / Li, L. / Ficarro, S.B. / Meyer, C.J. / Sinha, D. / You, I. / Tse, J. / He, Z. / Ji, W. / Che, J. / Kim, A.Y. / Yu, T. / Wen, K. / ...Authors: Lu, W. / Liu, Y. / Gao, Y. / Geng, Q. / Gurbani, D. / Li, L. / Ficarro, S.B. / Meyer, C.J. / Sinha, D. / You, I. / Tse, J. / He, Z. / Ji, W. / Che, J. / Kim, A.Y. / Yu, T. / Wen, K. / Anderson, K.C. / Marto, J.A. / Westover, K.D. / Zhang, T. / 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 | 7n8t.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n8t.ent.gz | 71 KB | Display | PDB format |
PDBx/mmJSON format | 7n8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n8t_validation.pdf.gz | 966.1 KB | Display | wwPDB validaton report |
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Full document | 7n8t_full_validation.pdf.gz | 967.3 KB | Display | |
Data in XML | 7n8t_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 7n8t_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/7n8t ftp://data.pdbj.org/pub/pdb/validation_reports/n8/7n8t | HTTPS FTP |
-Related structure data
Related structure data | 8elcC 3npcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40876.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK9, JNK2, PRKM9, SAPK1A / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P45984, mitogen-activated protein kinase |
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#2: Chemical | ChemComp-AMP / |
#3: Chemical | ChemComp-P6G / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.1 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→49.095 Å / Num. obs: 49432 / % possible obs: 99.48 % / Redundancy: 2.2 % / Biso Wilson estimate: 25.27 Å2 / CC1/2: 0.52 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.693→10 Å / Num. unique obs: 49432 / CC1/2: 0.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3npc Resolution: 1.69→49.09 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2588 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→49.09 Å
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Refine LS restraints |
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LS refinement shell |
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