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Yorodumi- PDB-3ws8: Crystal structure of PDE10A in complex with a benzimidazole inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ws8 | ||||||
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Title | Crystal structure of PDE10A in complex with a benzimidazole inhibitor | ||||||
Components | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / phosphodiesterase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Amano, Y. / Honbou, K. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2014 Title: Novel benzimidazole derivatives as phosphodiesterase 10A (PDE10A) inhibitors with improved metabolic stability. Authors: Chino, A. / Masuda, N. / Amano, Y. / Honbou, K. / Mihara, T. / Yamazaki, M. / Tomishima, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ws8.cif.gz | 144.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ws8.ent.gz | 113 KB | Display | PDB format |
PDBx/mmJSON format | 3ws8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ws8_validation.pdf.gz | 918.2 KB | Display | wwPDB validaton report |
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Full document | 3ws8_full_validation.pdf.gz | 936.6 KB | Display | |
Data in XML | 3ws8_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 3ws8_validation.cif.gz | 35.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/3ws8 ftp://data.pdbj.org/pub/pdb/validation_reports/ws/3ws8 | HTTPS FTP |
-Related structure data
Related structure data | 3ws9C 3wi2S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39606.430 Da / Num. of mol.: 2 / Fragment: catalytic domain, UNP RESIDUES 439-779 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE10A / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y233, 3',5'-cyclic-nucleotide phosphodiesterase, 3',5'-cyclic-GMP phosphodiesterase #2: Chemical | #3: Chemical | #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: 2.03 Å3/Da / Density % sol: 39.27 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 50mM Bis-tris propane pH6.0, 50mM Magnesium sulfate, 15% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→57.04 Å / Num. all: 18381 / Num. obs: 18381 / % possible obs: 89.6 % |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WI2 Resolution: 2.6→19.96 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.881 / SU B: 17.332 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 48.221 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.666 Å / Total num. of bins used: 20
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