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- PDB-7up6: Crystal structure of C-terminal domain of MSK1 in complex with in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7up6 | ||||||
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Title | Crystal structure of C-terminal domain of MSK1 in complex with in covalently bound literature RSK2 inhibitor pyrrolopyrimidine cyanoacrylamide compound 25 (co-crystal) | ||||||
![]() | Ribosomal protein S6 kinase alpha-5 | ||||||
![]() | TRANSFERASE / MSK1 / C-TERMINAL DOMAIN / PROTEIN KINASE / PHOSPHORYLATION | ||||||
Function / homology | ![]() histone H3S28 kinase activity / histone H2AS1 kinase activity / positive regulation of CREB transcription factor activity / CREB phosphorylation / histone H3S10 kinase activity / interleukin-1-mediated signaling pathway / negative regulation of cytokine production / regulation of postsynapse organization / ERK/MAPK targets / Recycling pathway of L1 ...histone H3S28 kinase activity / histone H2AS1 kinase activity / positive regulation of CREB transcription factor activity / CREB phosphorylation / histone H3S10 kinase activity / interleukin-1-mediated signaling pathway / negative regulation of cytokine production / regulation of postsynapse organization / ERK/MAPK targets / Recycling pathway of L1 / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / post-translational protein modification / axon guidance / positive regulation of NF-kappaB transcription factor activity / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yano, J.K. / Abendroth, J. / Hall, A. | ||||||
Funding support | 1items
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![]() | ![]() Title: Discovery and Characterization of a Novel Series of Chloropyrimidines as Covalent Inhibitors of the Kinase MSK1. Authors: Hall, A. / Abendroth, J. / Bolejack, M.J. / Ceska, T. / Dell'Aiera, S. / Ellis, V. / Fox 3rd, D. / Francois, C. / Muruthi, M.M. / Prevel, C. / Poullennec, K. / Romanov, S. / Valade, A. / ...Authors: Hall, A. / Abendroth, J. / Bolejack, M.J. / Ceska, T. / Dell'Aiera, S. / Ellis, V. / Fox 3rd, D. / Francois, C. / Muruthi, M.M. / Prevel, C. / Poullennec, K. / Romanov, S. / Valade, A. / Vanbellinghen, A. / Yano, J. / Geraerts, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.9 KB | Display | ![]() |
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PDB format | ![]() | 89.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 694.6 KB | Display | ![]() |
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Full document | ![]() | 695.4 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7up4C ![]() 7up5C ![]() 7up7C ![]() 7up8C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34668.809 Da / Num. of mol.: 1 / Fragment: Msk1 CTD 414-738 Delta Pro573-Pro596 GSG Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O75582, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-SUU / ( | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.8 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Crystals were produced by sitting drop vapor diffusion with an equal volume of the protein, Msk1-C terminal domain (PID6598-1, CID101276) at 4.91 mg/ml in 25mM HEPES pH 7.5, 150mM NaCl, 5% ...Details: Crystals were produced by sitting drop vapor diffusion with an equal volume of the protein, Msk1-C terminal domain (PID6598-1, CID101276) at 4.91 mg/ml in 25mM HEPES pH 7.5, 150mM NaCl, 5% Glycerol, 5mM BME and a crystallization buffer containing 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD: 20mM of each sodium formate, ammonium acetate, trisodium citrate, sodium-potassium tartrate, sodium oxamate: 100 mM MOPS / HEPES-Na pH 7.5 (tray ID 298849, well G8, Morpheus). Crystals were direly vitrified in in liquid N2. Puck ID BOW0-8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→35.59 Å / Num. obs: 12830 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 51.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.09 / Χ2: 1.026 / Net I/σ(I): 17.02 / Num. measured all: 98583 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2.82 / Num. measured obs: 1042 / Num. possible: 161 / Num. unique obs: 154 / CC1/2: 0.999 / Rrim(I) all: 0.037 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: in-house model Resolution: 2.6→35.59 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 23.1 / Stereochemistry target values: ML
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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 max: 158.58 Å2 / Biso mean: 61.88 Å2 / Biso min: 24.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→35.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.7 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
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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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