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Yorodumi- PDB-5i2r: human PDE10A in complex with 3-(2-phenylpyrazol-3-yl)-1-[3-(trifl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i2r | ||||||
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Title | human PDE10A in complex with 3-(2-phenylpyrazol-3-yl)-1-[3-(trifluoromethoxy)phenyl]pyridazin-4-one | ||||||
Components | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | ||||||
Keywords | HYDROLASE / PHOSPHODIESTERASE / PDE10 | ||||||
Function / homology | Function and homology information 3',5'-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 ...3',5'-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 / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Joseph, C. / Koerner, M. / Rudolph, M.G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i2r.cif.gz | 267.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i2r.ent.gz | 225.5 KB | Display | PDB format |
PDBx/mmJSON format | 5i2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/5i2r ftp://data.pdbj.org/pub/pdb/validation_reports/i2/5i2r | HTTPS FTP |
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-Related structure data
Related structure data | 5edbC 5edcC 5edeC 5edgC 5edhC 5ediC 5ezxC 5ezzC 5f00C 5f01C 5f02C 5f03C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 36774.414 Da / Num. of mol.: 4 / Fragment: UNP residues 457-773 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE10A / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9Y233, 3',5'-cyclic-nucleotide phosphodiesterase, 3',5'-cyclic-GMP phosphodiesterase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-67A / #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: 2.87 Å3/Da / Density % sol: 57.15 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: none |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 31, 1970 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→43.68 Å / Num. obs: 55869 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.1106 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 3.04 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 1.27 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Resolution: 2.5→35.44 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.438 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.544 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||
Displacement parameters | Biso mean: 37.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→35.44 Å
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LS refinement shell | Resolution: 2.5→2.57 Å / Total num. of bins used: 20
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