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Yorodumi- PDB-4l9i: Bovine G Protein Coupled Receptor Kinase 1 in Complex with Paroxetine -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l9i | ||||||
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Title | Bovine G Protein Coupled Receptor Kinase 1 in Complex with Paroxetine | ||||||
Components | Rhodopsin kinase | ||||||
Keywords | Transferase / membrane protein/inhibitor / AGC family kinase / SER/THR KINASE / RGS HOMOLOGY DOMAIN / G PROTEIN COUPLED RECEPTOR KINASE / GRK / GRK1 / RHODOPSIN KINASE / SSRI / HYDROLYASE / GPCR / PHOSPHORYLATION / membrane protein-inhibitor complex | ||||||
Function / homology | Function and homology information rhodopsin kinase / rhodopsin kinase activity / regulation of opsin-mediated signaling pathway / Inactivation, recovery and regulation of the phototransduction cascade / regulation of signal transduction / visual perception / photoreceptor disc membrane / protein autophosphorylation / signal transduction / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Homan, K.T. / Tesmer, J.J.G. | ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2014 Title: Structural and functional analysis of g protein-coupled receptor kinase inhibition by paroxetine and a rationally designed analog. Authors: Homan, K.T. / Wu, E. / Wilson, M.W. / Singh, P. / 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 | 4l9i.cif.gz | 428.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l9i.ent.gz | 352.5 KB | Display | PDB format |
PDBx/mmJSON format | 4l9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l9i_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4l9i_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4l9i_validation.xml.gz | 39.9 KB | Display | |
Data in CIF | 4l9i_validation.cif.gz | 57 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/4l9i ftp://data.pdbj.org/pub/pdb/validation_reports/l9/4l9i | HTTPS FTP |
-Related structure data
Related structure data | 4mk0C 3c4zS C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 57355.559 Da / Num. of mol.: 2 / Fragment: unp residues 30-533 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK1, RHOK / Plasmid: PFastBacDual / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P28327, rhodopsin kinase #2: Chemical | #3: Chemical | ChemComp-MES / | #4: Chemical | #5: 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: 2.72 Å3/Da / Density % sol: 54.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.75 Details: 12% PEG3350, 1M NaCl, pH 5.75, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1.0793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 21, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.32→50 Å / Num. all: 54845 / Num. obs: 54845 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3C4Z Resolution: 2.32→29.93 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.197 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.22 / 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: 45.787 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.32→29.93 Å
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Refine LS restraints |
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