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Yorodumi- PDB-8uap: Crystal Structure of Human G Protein-Coupled Receptor Kinase 5 D3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8uap | |||||||||
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Title | Crystal Structure of Human G Protein-Coupled Receptor Kinase 5 D311N in Complex with CCG273441 | |||||||||
Components | G protein-coupled receptor kinase 5 | |||||||||
Keywords | SIGNALING PROTEIN/INHIBITOR / G protein-coupled receptor / GPCR G protein-coupled receptor kinase / GRK kinase / SIGNALING PROTEIN-INHIBITOR complex | |||||||||
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 / regulation of G protein-coupled receptor signaling pathway / fat cell differentiation / regulation of signal transduction / protein kinase C binding / phospholipid binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway ...G-protein-coupled receptor kinase / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / tachykinin receptor signaling pathway / regulation of G protein-coupled receptor signaling pathway / fat cell differentiation / regulation of signal transduction / protein kinase C binding / phospholipid binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Wnt signaling pathway / G alpha (s) signalling events / G alpha (q) signalling events / nuclear membrane / protein autophosphorylation / regulation of cell cycle / protein kinase activity / nuclear speck / G protein-coupled receptor signaling pathway / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / ATP binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Chen, Y. / Tesmer, J.J.G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2023 Title: Development of a new class of potent and highly selective G protein-coupled receptor kinase 5 inhibitors and structural insight from crystal structures of inhibitor complexes. Authors: Chen, Y. / Sonawane, A. / Manda, R. / Gadi, R.K. / Tesmer, J.J.G. / Ghosh, A.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8uap.cif.gz | 373 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8uap.ent.gz | 257.4 KB | Display | PDB format |
PDBx/mmJSON format | 8uap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/8uap ftp://data.pdbj.org/pub/pdb/validation_reports/ua/8uap | HTTPS FTP |
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-Related structure data
Related structure data | 8uaqC 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: 68931.727 Da / Num. of mol.: 1 / Mutation: D311N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GRK5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P34947 |
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#2: Chemical | ChemComp-W2T / ( |
#3: 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: 2.45 Å3/Da / Density % sol: 49.79 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 220 mM potassium citrate tribasic, 20% PEG3350, crystals soaked in 25% PEG3350, 10% glycerol, 1 mM inhibitor |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→63.1 Å / Num. obs: 27696 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 70.8 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.39→2.47 Å / Num. unique obs: 2700 / CC1/2: 0.939 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→24.74 Å / SU ML: 0.3959 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1244 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→24.74 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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