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Yorodumi- PDB-4msa: Crystal structure of PDE10A2 with fragment ZT0449 (5-nitro-1H-ben... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4msa | ||||||
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Title | Crystal structure of PDE10A2 with fragment ZT0449 (5-nitro-1H-benzimidazole) | ||||||
Components | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / fragment screening / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Sridar, V. / Badger, J. / Logan, C. / Chie-Leon, B. / Nienaber, V. | ||||||
Citation | Journal: J Biomol Screen / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4msa.cif.gz | 151.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4msa.ent.gz | 117.7 KB | Display | PDB format |
PDBx/mmJSON format | 4msa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4msa_validation.pdf.gz | 451.9 KB | Display | wwPDB validaton report |
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Full document | 4msa_full_validation.pdf.gz | 454.4 KB | Display | |
Data in XML | 4msa_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 4msa_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/4msa ftp://data.pdbj.org/pub/pdb/validation_reports/ms/4msa | HTTPS FTP |
-Related structure data
Related structure data | 4lkqC 4lljC 4llkC 4llpC 4llxC 4lm0C 4lm1C 4lm2C 4lm3C 4lm4C 4mrwC 4mrzC 4ms0C 4mscC 4mseC 4mshC 4msnC 2ourS 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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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.) Homo sapiens (human) / Gene: PDE10A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q9Y233, 3',5'-cyclic-nucleotide phosphodiesterase, 3',5'-cyclic-GMP phosphodiesterase #2: Chemical | #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.46 % |
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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: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 31, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. all: 80392 / Num. obs: 80392 / % possible obs: 96.1 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -4 / Redundancy: 4.1 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.62→1.68 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.5 / Num. unique all: 8042 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2OUR Resolution: 1.62→43.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.98 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.099 / 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: 24.934 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→43.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.663 Å / Total num. of bins used: 20 /
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