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- PDB-5edi: human PDE10A, 6-Chloro-5,8-dimethyl-2-[2-(2-methyl-5-pyrrolidin-1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5edi | ||||||
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Title | human PDE10A, 6-Chloro-5,8-dimethyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-2H-[1,2,4]triazol-3-yl)-ethyl]-[1,2,4]triazolo[1,5-a]pyridine, 2.20A, H3, Rfree=23.5% | ||||||
![]() | (cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase ...) x 2 | ||||||
![]() | HYDROLASE / PHOSPHODIESTERASE / PDE10 | ||||||
Function / homology | ![]() cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / cGMP catabolic process / cGMP effects / cAMP catabolic process / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity ...cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / cGMP catabolic process / cGMP effects / cAMP catabolic process / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP binding / cAMP-mediated signaling / G alpha (s) signalling events / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joseph, C. / Rudolph, M.G. | ||||||
![]() | ![]() Title: A Real-World Perspective on Molecular Design. Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / ...Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / Schulz-Gasch, T. / Woltering, T. / Stahl, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.4 KB | Display | ![]() |
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PDB format | ![]() | 223.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 49.3 KB | Display | |
Data in CIF | ![]() | 67.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5edbC ![]() 5edcC ![]() 5edeC ![]() 5edgC ![]() 5edhC ![]() 5ezxC ![]() 5ezzC ![]() 5f00C ![]() 5f01C ![]() 5f02C ![]() 5f03C ![]() 5i2rC 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-CAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase ... , 2 types, 4 molecules ACDB
#1: Protein | Mass: 37090.688 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9Y233, 3',5'-cyclic-nucleotide phosphodiesterase, 3',5'-cyclic-GMP phosphodiesterase #2: Protein | | Mass: 37161.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9Y233, 3',5'-cyclic-nucleotide phosphodiesterase, 3',5'-cyclic-GMP phosphodiesterase |
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-Non-polymers , 4 types, 389 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/5M9.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/5M9.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-5M9 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.92 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES-NaOH pH 7.5, 30% PEG550MME, 50mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2012 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→43.68 Å / Num. obs: 81492 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.22 % / Biso Wilson estimate: 54.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.077 / Rsym value: 0.058 / Χ2: 0.971 / Net I/σ(I): 16.86 / Num. measured all: 474200 | |||||||||
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 5.15 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 1.29 / Num. measured obs: 5202 / Num. possible: 1028 / Num. unique obs: 1018 / CC1/2: 1 / Rrim(I) all: 0.017 / Rsym value: 0.714 / Rejects: 0 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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: 80 Å2 / Biso mean: 53.039 Å2 / Biso min: 24.76 Å2
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Refinement step | Cycle: final / Resolution: 2.2→43.6 Å
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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