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Yorodumi- PDB-4wnk: Crystal Structure of Bovine G Protein Coupled-Receptor Kinase 5 i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wnk | ||||||||||||
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Title | Crystal Structure of Bovine G Protein Coupled-Receptor Kinase 5 in Complex with CCG215022 | ||||||||||||
Components | G protein-coupled receptor kinase 5 | ||||||||||||
Keywords | LIGASE / G protein-coupled receptor kinase 5 / hydrolase / phosphorylation / cardiovascular disease | ||||||||||||
Function / homology | Function and homology information G-protein-coupled receptor kinase / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / tachykinin receptor signaling pathway / G alpha (s) signalling events / fat cell differentiation / Wnt signaling pathway / nuclear membrane / protein autophosphorylation / regulation of cell cycle ...G-protein-coupled receptor kinase / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / tachykinin receptor signaling pathway / G alpha (s) signalling events / fat cell differentiation / Wnt signaling pathway / nuclear membrane / protein autophosphorylation / regulation of cell cycle / nuclear speck / protein serine/threonine kinase activity / lipid binding / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||||||||
Authors | Homan, K.T. / Tesmer, J.J.G. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Crystal Structure of G Protein-coupled Receptor Kinase 5 in Complex with a Rationally Designed Inhibitor. Authors: Homan, K.T. / Waldschmidt, H.V. / Glukhova, A. / Cannavo, A. / Song, J. / Cheung, J.Y. / Koch, W.J. / Larsen, S.D. / Tesmer, J.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wnk.cif.gz | 225.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wnk.ent.gz | 180.8 KB | Display | PDB format |
PDBx/mmJSON format | 4wnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/4wnk ftp://data.pdbj.org/pub/pdb/validation_reports/wn/4wnk | HTTPS FTP |
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-Related structure data
Related structure data | 4pnkS 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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Details | Monomeric G protein coupled-receptor kinase 5 as evidenced by gel filtration |
-Components
#1: Protein | Mass: 69037.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK5, GPRK5 / Plasmid: PFastBacDual / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P43249, G-protein-coupled receptor kinase |
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#2: Chemical | ChemComp-453 / ( |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.5 / Details: HEPES, ethylene glycol, PEG 3350 / PH range: 7.25-7.75 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1.1271 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→50 Å / Num. all: 24217 / Num. obs: 24217 / % possible obs: 99.9 % / Redundancy: 37.7 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 42.3 |
Reflection shell | Resolution: 2.42→2.46 Å / Redundancy: 34.8 % / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PNK Resolution: 2.42→24.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 20.69 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.266 Å2
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Refinement step | Cycle: LAST / Resolution: 2.42→24.47 Å
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