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Yorodumi- PDB-3sl4: Crystal structure of the catalytic domain of PDE4D2 with compound 10D -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sl4 | ||||||
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Title | Crystal structure of the catalytic domain of PDE4D2 with compound 10D | ||||||
Components | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | ||||||
Keywords | Hydrolase/Inhibitor / catalytic mechanism / cAMP hydrolysis / Hydrolase-Inhibitor complex | ||||||
Function / homology | Function and homology information signaling receptor regulator activity / negative regulation of relaxation of cardiac muscle / negative regulation of heart contraction / 3',5'-cyclic-AMP phosphodiesterase / positive regulation of interleukin-5 production / regulation of cardiac muscle cell contraction / establishment of endothelial barrier / negative regulation of cAMP-mediated signaling / beta-2 adrenergic receptor binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel ...signaling receptor regulator activity / negative regulation of relaxation of cardiac muscle / negative regulation of heart contraction / 3',5'-cyclic-AMP phosphodiesterase / positive regulation of interleukin-5 production / regulation of cardiac muscle cell contraction / establishment of endothelial barrier / negative regulation of cAMP-mediated signaling / beta-2 adrenergic receptor binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of heart rate / heterocyclic compound binding / adrenergic receptor signaling pathway / voltage-gated calcium channel complex / regulation of cell communication by electrical coupling involved in cardiac conduction / cAMP catabolic process / calcium channel regulator activity / cAMP-mediated signaling / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / DARPP-32 events / negative regulation of peptidyl-serine phosphorylation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cAMP binding / cellular response to cAMP / cellular response to epinephrine stimulus / calcium channel complex / positive regulation of interleukin-2 production / regulation of heart rate / positive regulation of type II interferon production / ATPase binding / T cell receptor signaling pathway / G alpha (s) signalling events / scaffold protein binding / transmembrane transporter binding / apical plasma membrane / centrosome / perinuclear region of cytoplasm / enzyme binding / signal transduction / membrane / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molrep / Resolution: 1.9 Å | ||||||
Authors | Feil, S.F. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: Thiophene inhibitors of PDE4: Crystal structures show a second binding mode at the catalytic domain of PDE4D2. Authors: Nankervis, J.L. / Feil, S.C. / Hancock, N.C. / Zheng, Z. / Ng, H.L. / Morton, C.J. / Holien, J.K. / Ho, P.W. / Frazzetto, M.M. / Jennings, I.G. / Manallack, D.T. / Martin, T.J. / Thompson, P.E. / Parker, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sl4.cif.gz | 297.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sl4.ent.gz | 238.5 KB | Display | PDB format |
PDBx/mmJSON format | 3sl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/3sl4 ftp://data.pdbj.org/pub/pdb/validation_reports/sl/3sl4 | HTTPS FTP |
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-Related 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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Details | AS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41523.887 Da / Num. of mol.: 4 / Fragment: Catalytic domain, UNP residues 381-741 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE4D, DPDE3 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star Rosetta References: UniProt: Q08499, 3',5'-cyclic-nucleotide phosphodiesterase |
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-Non-polymers , 8 types, 549 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-DMS / #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-PO4 / #7: Chemical | ChemComp-JN4 / #8: Chemical | #9: 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: 2.93 Å3/Da / Density % sol: 57.99 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 25% (v/v) ethylene glycol, 10% (v/v) isopropanol, 100 mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 17, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: K-B pair of biomorph mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 139220 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.065 / Χ2: 1.063 / Net I/σ(I): 10.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: molrep / Resolution: 1.9→32.621 Å / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.8499 / SU ML: 0.25 / σ(F): 0.05 / Phase error: 22.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.572 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.64 Å2 / Biso mean: 32.3233 Å2 / Biso min: 10.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→32.621 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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