+Open data
-Basic information
Entry | Database: PDB / ID: 6ko1 | ||||||||||||||||||
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Title | The crystal structue of PDE10A complexed with 2d | ||||||||||||||||||
Components | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | ||||||||||||||||||
Keywords | HYDROLASE / PDE10A inhibitor | ||||||||||||||||||
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: 2.7 Å | ||||||||||||||||||
Authors | Huang, Y.-Y. / Yu, Y.F. / Zhang, C. / Guo, L. / Wu, D. / Luo, H.-B. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Acs Chem Neurosci / Year: 2020 Title: Discovery and Optimization of Chromone Derivatives as Novel Selective Phosphodiesterase 10 Inhibitors. Authors: Yu, Y.F. / Zhang, C. / Huang, Y.Y. / Zhang, S. / Zhou, Q. / Li, X. / Lai, Z. / Li, Z. / Gao, Y. / Wu, Y. / Guo, L. / Wu, D. / Luo, H.B. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ko1.cif.gz | 143.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ko1.ent.gz | 110 KB | Display | PDB format |
PDBx/mmJSON format | 6ko1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ko1_validation.pdf.gz | 945.1 KB | Display | wwPDB validaton report |
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Full document | 6ko1_full_validation.pdf.gz | 960 KB | Display | |
Data in XML | 6ko1_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 6ko1_validation.cif.gz | 35.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/6ko1 ftp://data.pdbj.org/pub/pdb/validation_reports/ko/6ko1 | HTTPS FTP |
-Related structure data
Related structure data | 6ko0C 2oupS S: Starting model for refinement C: citing same article (ref.) |
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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: 37292.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE10A / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q9Y233, 3',5'-cyclic-nucleotide phosphodiesterase, 3',5'-cyclic-GMP phosphodiesterase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.23 Å3/Da / Density % sol: 44.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: 0.1 M Hepes (pH 7.5), 0.2 M MgCl2, 18% PEG 3350, 50 mM 2-mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.5418 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Jan 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→24.823 Å / Num. obs: 18454 / % possible obs: 98.82 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.063408668 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1792 / % possible all: 96.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OUP Resolution: 2.7→24.823 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 34.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.85 Å2 / Biso mean: 26.9051 Å2 / Biso min: 7.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→24.823 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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