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Yorodumi- PDB-6es0: Crystal structure of the kinase domain of human RIPK2 in complex ... -
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-Basic information
Entry | Database: PDB / ID: 6es0 | ||||||
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Title | Crystal structure of the kinase domain of human RIPK2 in complex with the activation loop targeting inhibitor CS-R35 | ||||||
Components | Receptor-interacting serine/threonine-protein kinase 2 | ||||||
Keywords | TRANSFERASE / Kinase Inhibitor | ||||||
Function / homology | Function and homology information response to interleukin-18 / positive regulation of T-helper 1 cell differentiation / toll-like receptor 2 signaling pathway / positive regulation of cytokine-mediated signaling pathway / immature T cell proliferation in thymus / positive regulation of T-helper 1 type immune response / positive regulation of xenophagy / LIM domain binding / xenophagy / CD4-positive, alpha-beta T cell proliferation ...response to interleukin-18 / positive regulation of T-helper 1 cell differentiation / toll-like receptor 2 signaling pathway / positive regulation of cytokine-mediated signaling pathway / immature T cell proliferation in thymus / positive regulation of T-helper 1 type immune response / positive regulation of xenophagy / LIM domain binding / xenophagy / CD4-positive, alpha-beta T cell proliferation / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of protein K63-linked ubiquitination / positive regulation of stress-activated MAPK cascade / cellular response to muramyl dipeptide / CARD domain binding / positive regulation of immature T cell proliferation in thymus / caspase binding / JUN kinase kinase kinase activity / cellular response to peptidoglycan / response to interleukin-12 / positive regulation of CD4-positive, alpha-beta T cell proliferation / activation of cysteine-type endopeptidase activity / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of macrophage cytokine production / toll-like receptor 4 signaling pathway / response to exogenous dsRNA / cellular response to lipoteichoic acid / canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / signaling adaptor activity / stress-activated MAPK cascade / positive regulation of chemokine production / JNK cascade / lipopolysaccharide-mediated signaling pathway / p75NTR recruits signalling complexes / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / positive regulation of interleukin-2 production / positive regulation of interferon-beta production / response to interleukin-1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-1 beta production / positive regulation of protein ubiquitination / activated TAK1 mediates p38 MAPK activation / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / TAK1-dependent IKK and NF-kappa-B activation / non-membrane spanning protein tyrosine kinase activity / NOD1/2 Signaling Pathway / protein homooligomerization / cytokine-mediated signaling pathway / Interleukin-1 signaling / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of type II interferon production / Ovarian tumor domain proteases / Downstream TCR signaling / positive regulation of protein binding / positive regulation of peptidyl-serine phosphorylation / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / vesicle / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / non-specific serine/threonine protein kinase / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / positive regulation of apoptotic process / phosphorylation / innate immune response / protein serine kinase activity / signaling receptor binding / protein serine/threonine kinase activity / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Pinkas, D.M. / Bufton, J.C. / Suebsuwong, C. / Ray, S.S. / Dai, B. / Newman, J.A. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Pinkas, D.M. / Bufton, J.C. / Suebsuwong, C. / Ray, S.S. / Dai, B. / Newman, J.A. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Degterev, A. / Cuny, G.D. / Bullock, A.N. | ||||||
Citation | Journal: Bioorg. Med. Chem. Lett. / Year: 2018 Title: Activation loop targeting strategy for design of receptor-interacting protein kinase 2 (RIPK2) inhibitors. Authors: Suebsuwong, C. / Pinkas, D.M. / Ray, S.S. / Bufton, J.C. / Dai, B. / Bullock, A.N. / Degterev, A. / Cuny, G.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6es0.cif.gz | 132.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6es0.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 6es0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6es0_validation.pdf.gz | 861.2 KB | Display | wwPDB validaton report |
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Full document | 6es0_full_validation.pdf.gz | 866.6 KB | Display | |
Data in XML | 6es0_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 6es0_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/6es0 ftp://data.pdbj.org/pub/pdb/validation_reports/es/6es0 | HTTPS FTP |
-Related structure data
Related structure data | 4c8bS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36385.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RIPK2, CARDIAK, RICK, RIP2, UNQ277/PRO314/PRO34092 / Production host: Escherichia coli (E. coli) References: UniProt: O43353, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 25% PEG Smear Low -- 0.1M MES pH 6.5 -- 0.05M magnesium acetate -- 0.05M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→71.74 Å / Num. obs: 29591 / % possible obs: 99.41 % / Redundancy: 4.6 % / Net I/σ(I): 16.05 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4C8B Resolution: 2.38→71.74 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / Phase error: 25.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→71.74 Å
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Refine LS restraints |
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LS refinement shell |
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