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- PDB-4msn: Crystal structure of PDE10A2 with fragment ZT0451 (8-nitroquinoline) -
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Open data
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Basic information
Entry | Database: PDB / ID: 4msn | ||||||
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Title | Crystal structure of PDE10A2 with fragment ZT0451 (8-nitroquinoline) | ||||||
![]() | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / fragment screening / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sridhar, V. / Badger, J. / Logan, C. / Chie-Leon, B. / Nienaber, V. | ||||||
![]() | ![]() Title: Identification and optimization of PDE10A inhibitors using fragment-based screening by nanocalorimetry and X-ray crystallography. Authors: Recht, M.I. / Sridhar, V. / Badger, J. / Bounaud, P.Y. / Logan, C. / Chie-Leon, B. / Nienaber, V. / Torres, F.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.6 KB | Display | ![]() |
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PDB format | ![]() | 112.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4lkqC ![]() 4lljC ![]() 4llkC ![]() 4llpC ![]() 4llxC ![]() 4lm0C ![]() 4lm1C ![]() 4lm2C ![]() 4lm3C ![]() 4lm4C ![]() 4mrwC ![]() 4mrzC ![]() 4ms0C ![]() 4msaC ![]() 4mscC ![]() 4mseC ![]() 4mshC ![]() 2ourS C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 39479.242 Da / Num. of mol.: 2 / Fragment: catalytic domain, UNP residues 439-779 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: Chemical | ChemComp-2ZQ / | #3: Chemical | ChemComp-NI / #4: Water | ChemComp-HOH / | Nonpolymer details | THE FOUR DIVALENT CATIONS ARE REPRESENTE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18% PEG 4450, 0.2M calcium acetate, 50mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 9, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.73 Å / Num. all: 28032 / Num. obs: 28032 / % possible obs: 95.8 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -4 / Redundancy: 4.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3935 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2OUR Resolution: 2.3→39.73 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.883 / SU B: 10.801 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R: 0.559 / ESU R Free: 0.303 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.357 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→39.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20 /
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