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- PDB-5edh: human PDE10A, 8-ethyl-5-methyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5edh | ||||||
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Title | human PDE10A, 8-ethyl-5-methyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-[1,2,4]triazolo[1,5-c]pyrimidine, 2.03A, H3, Rfree=22.7% | ||||||
![]() | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | ||||||
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Function / homology | ![]() cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 268.3 KB | Display | ![]() |
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PDB format | ![]() | 225.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5edbC ![]() 5edcC ![]() 5edeC ![]() 5edgC ![]() 5ediC ![]() 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
#1: Protein | Mass: 36515.152 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9Y233, ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-5MF / #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.59 % |
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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: May 17, 2013 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.03→43.68 Å / Num. obs: 103725 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.17 % / Biso Wilson estimate: 44.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.084 / Rsym value: 0.069 / Χ2: 0.988 / Net I/σ(I): 14.8 / Num. measured all: 548572 | |||||||||
Reflection shell | Resolution: 2.03→2.13 Å / Redundancy: 5.05 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 1.28 / Num. measured obs: 6324 / Num. possible: 1183 / Num. unique obs: 1173 / CC1/2: 1 / Rrim(I) all: 0.018 / Rsym value: 0.742 / Rejects: 0 / % possible all: 99.6 |
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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: 40.871 Å2 / Biso min: 18.84 Å2
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Refinement step | Cycle: final / Resolution: 2.03→43.68 Å
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LS refinement shell | Resolution: 2.03→2.083 Å / Total num. of bins used: 20
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