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- PDB-5om1: Structure of the A2A-StaR2-bRIL562-Compound 4e complex at 2.1A ob... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5om1 | ||||||
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Title | Structure of the A2A-StaR2-bRIL562-Compound 4e complex at 2.1A obtained from in meso soaking experiments (1 hour soak). | ||||||
![]() | Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a | ||||||
![]() | MEMBRANE PROTEIN / G-Protein Coupled Receptor / Adenosine 2a receptor / 7 TM integral membrane protein / thermostabilizing mutations | ||||||
Function / homology | ![]() positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / NGF-independant TRKA activation ...positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / NGF-independant TRKA activation / Surfactant metabolism / positive regulation of urine volume / synaptic transmission, dopaminergic / : / inhibitory postsynaptic potential / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / synaptic transmission, cholinergic / blood circulation / positive regulation of glutamate secretion / response to caffeine / intermediate filament / eating behavior / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / : / cellular defense response / prepulse inhibition / phagocytosis / response to amphetamine / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / excitatory postsynaptic potential / positive regulation of apoptotic signaling pathway / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / positive regulation of long-term synaptic potentiation / central nervous system development / locomotory behavior / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / astrocyte activation / apoptotic signaling pathway / electron transport chain / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / vasodilation / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / postsynaptic membrane / negative regulation of neuron apoptotic process / periplasmic space / electron transfer activity / calmodulin binding / response to xenobiotic stimulus / inflammatory response / iron ion binding / negative regulation of cell population proliferation / neuronal cell body / lipid binding / glutamatergic synapse / dendrite / heme binding / regulation of DNA-templated transcription / protein-containing complex binding / apoptotic process / enzyme binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rucktooa, P. / Cheng, R.K.Y. / Segala, E. / Geng, T. / Errey, J.C. / Brown, G.A. / Cooke, R. / Marshall, F.H. / Dore, A.S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Towards high throughput GPCR crystallography: In Meso soaking of Adenosine A2A Receptor crystals. Authors: Rucktooa, P. / Cheng, R.K.Y. / Segala, E. / Geng, T. / Errey, J.C. / Brown, G.A. / Cooke, R.M. / Marshall, F.H. / Dore, A.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191.1 KB | Display | ![]() |
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PDB format | ![]() | 151.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5olgC ![]() 5olhC ![]() 5oloC ![]() 5olvC ![]() 5olzC ![]() 5om4C ![]() 5mzjS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48067.824 Da / Num. of mol.: 1 Mutation: A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; ...Mutation: A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: ADORA2A, ADORA2, cybC / Production host: ![]() |
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-Non-polymers , 7 types, 170 molecules ![](data/chem/img/T4E.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-T4E / | ||||||||
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#3: Chemical | ChemComp-NA / | ||||||||
#4: Chemical | ChemComp-OLA / #5: Chemical | ChemComp-CLR / #6: Chemical | ChemComp-OLC / ( #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.6 % |
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Crystal grow | Temperature: 293.15 K / Method: lipidic cubic phase Details: Crystal growth: 0.l M tri-sodium citrate pH 5.3-5.4, 0.05 M sodium thiocyanate, 29-32% PEG400, 2% (v/v) 2,5-hexanediol and 0.5 mM theophylline Compound 4e was added to the mother liquor to a ...Details: Crystal growth: 0.l M tri-sodium citrate pH 5.3-5.4, 0.05 M sodium thiocyanate, 29-32% PEG400, 2% (v/v) 2,5-hexanediol and 0.5 mM theophylline Compound 4e was added to the mother liquor to a concentration of 0.005 mM for the soaking experiments. PH range: 5.3-5.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96857 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→33.83 Å / Num. obs: 29886 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.061 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.355 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2394 / CC1/2: 0.524 / Rpim(I) all: 0.564 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MZJ Resolution: 2.1→33.83 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 20.09 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→33.83 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 |
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