+Open data
-Basic information
Entry | Database: PDB / ID: 5b25 | ||||||
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Title | Crystal structure of human PDE1B with inhibitor 3 | ||||||
Components | Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Hydrolase / Inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / cellular response to macrophage colony-stimulating factor stimulus / serotonin metabolic process / dopamine catabolic process / cellular response to granulocyte macrophage colony-stimulating factor stimulus / monocyte differentiation / Cam-PDE 1 activation / 3',5'-cyclic-nucleotide phosphodiesterase / cGMP effects ...calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / cellular response to macrophage colony-stimulating factor stimulus / serotonin metabolic process / dopamine catabolic process / cellular response to granulocyte macrophage colony-stimulating factor stimulus / monocyte differentiation / Cam-PDE 1 activation / 3',5'-cyclic-nucleotide phosphodiesterase / cGMP effects / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / response to amphetamine / cAMP-mediated signaling / locomotory behavior / visual learning / G alpha (s) signalling events / calmodulin binding / neuronal cell body / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ida, K. / Lane, W. / Snell, G. / Sogabe, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Discovery of Potent and Selective Inhibitors of Phosphodiesterase 1 for the Treatment of Cognitive Impairment Associated with Neurodegenerative and Neuropsychiatric Diseases Authors: Li, P. / Zheng, H. / Zhao, J. / Zhang, L. / Yao, W. / Zhu, H. / Beard, J.D. / Ida, K. / Lane, W. / Snell, G. / Sogabe, S. / Heyser, C.J. / Snyder, G.L. / Hendrick, J.P. / Vanover, K.E. / ...Authors: Li, P. / Zheng, H. / Zhao, J. / Zhang, L. / Yao, W. / Zhu, H. / Beard, J.D. / Ida, K. / Lane, W. / Snell, G. / Sogabe, S. / Heyser, C.J. / Snyder, G.L. / Hendrick, J.P. / Vanover, K.E. / Davis, R.E. / Wennogle, L.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b25.cif.gz | 558.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b25.ent.gz | 460.2 KB | Display | PDB format |
PDBx/mmJSON format | 5b25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b25_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5b25_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5b25_validation.xml.gz | 57 KB | Display | |
Data in CIF | 5b25_validation.cif.gz | 82.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/5b25 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/5b25 | HTTPS FTP |
-Related structure data
Related structure data | 1tazS 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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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 38574.164 Da / Num. of mol.: 4 / Fragment: UNP residues 146-506 / Mutation: DEL449-471 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE1B, PDE1B1, PDES1B / Plasmid: pE-SUMOpro Amp / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q01064, 3',5'-cyclic-nucleotide phosphodiesterase |
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-Non-polymers , 6 types, 941 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-4QJ / ( #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-GOL / #7: 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: 2.54 Å3/Da / Density % sol: 51.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.75 M ammonium sulfate, 0.1 M Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976486 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976486 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 125166 / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.102 / Χ2: 1.011 / Net I/av σ(I): 16.157 / Net I/σ(I): 7.9 / Num. measured all: 723862 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TAZ Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.1933 / WRfactor Rwork: 0.164 / FOM work R set: 0.8524 / SU B: 6.094 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1361 / SU Rfree: 0.1243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
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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 max: 123.35 Å2 / Biso mean: 27.414 Å2 / Biso min: 11.86 Å2
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Refinement step | Cycle: final / Resolution: 1.9→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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