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- PDB-3pvw: Bovine GRK2 in complex with Gbetagamma subunits and a selective k... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pvw | ||||||
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Title | Bovine GRK2 in complex with Gbetagamma subunits and a selective kinase inhibitor (CMPD103A) | ||||||
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![]() | TRANSFERASE/SIGNALING PROTEIN/INHIBITOR / Transferase / Serine/threonine-protein kinase / ATP-binding / Inhibitor / Membrane / TRANSFERASE-SIGNALING PROTEIN-INHIBITOR complex | ||||||
Function / homology | ![]() Calmodulin induced events / beta-adrenergic-receptor kinase / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / Activation of SMO / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / Edg-2 lysophosphatidic acid receptor binding / alpha-2A adrenergic receptor binding / Olfactory Signaling Pathway ...Calmodulin induced events / beta-adrenergic-receptor kinase / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / Activation of SMO / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / Edg-2 lysophosphatidic acid receptor binding / alpha-2A adrenergic receptor binding / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / negative regulation of striated muscle contraction / desensitization of G protein-coupled receptor signaling pathway / positive regulation of protein localization to cilium / Cargo recognition for clathrin-mediated endocytosis / regulation of the force of heart contraction / Activation of the phototransduction cascade / positive regulation of smoothened signaling pathway / G protein-coupled receptor internalization / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / regulation of signal transduction / cardiac muscle contraction / cell projection / G protein-coupled receptor binding / intracellular protein transport / G protein-coupled acetylcholine receptor signaling pathway / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / presynapse / postsynapse / peptidyl-serine phosphorylation / protein kinase activity / G protein-coupled receptor signaling pathway / protein phosphorylation / GTPase activity / ATP binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thal, D.M. / Tesmer, J.J. | ||||||
![]() | ![]() Title: Molecular Mechanism of Selectivity among G Protein-Coupled Receptor Kinase 2 Inhibitors. Authors: Thal, D.M. / Yeow, R.Y. / Schoenau, C. / Huber, J. / Tesmer, J.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 421.3 KB | Display | ![]() |
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PDB format | ![]() | 348.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 740.2 KB | Display | ![]() |
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Full document | ![]() | 754.7 KB | Display | |
Data in XML | ![]() | 36.4 KB | Display | |
Data in CIF | ![]() | 49.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pscC ![]() 3pvuC ![]() 1omwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 80578.820 Da / Num. of mol.: 1 / Mutation: S670A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P21146, beta-adrenergic-receptor kinase |
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#2: Protein | Mass: 37416.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 8406.658 Da / Num. of mol.: 1 / Fragment: UNP residues 1-68 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Chemical | ChemComp-QRX / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: 7% PEG3350, 250 mM NaCl, 100 mM MES pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 150 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 1, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.49→30 Å / Num. obs: 50352 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.072 / Χ2: 1.385 / Net I/σ(I): 20.45 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OMW Resolution: 2.49→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2741 / WRfactor Rwork: 0.227 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.747 / SU B: 28.961 / SU ML: 0.277 / SU R Cruickshank DPI: 0.4518 / SU Rfree: 0.3053 / Cross valid method: THROUGHOUT / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 205.86 Å2 / Biso mean: 79.0688 Å2 / Biso min: 37.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.492→2.557 Å / Total num. of bins used: 20
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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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