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Yorodumi- PDB-3v9b: Crystal structure of the catalytic domain of PDE4D2 with (S)-N-(3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v9b | ||||||
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Title | Crystal structure of the catalytic domain of PDE4D2 with (S)-N-(3-{1-[1-(3-Cyclopropylmethoxy-4-difluoromethoxyphenyl)-2-(1-oxypyridin-4-yl)-ethyl]-1H-pyrazl-3-yl}phenyl)acetamide | ||||||
Components | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / hydrolase / 3' / 5'-Cyclic-AMP Phosphodiesterases / Cyclic nucleotide / phosphodiesterases / HYDROLASE-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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kim, H.T. / Chang, H.J. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2012 Title: Stereoselective synthesis of novel pyrazole derivatives using tert-butansulfonamide as a chiral auxiliary Authors: Park, C.M. / Jeon, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v9b.cif.gz | 281.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v9b.ent.gz | 226.3 KB | Display | PDB format |
PDBx/mmJSON format | 3v9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/3v9b ftp://data.pdbj.org/pub/pdb/validation_reports/v9/3v9b | HTTPS FTP |
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-Related structure data
Related structure data | 3sl8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 41394.773 Da / Num. of mol.: 4 / Fragment: catalytic domain, UNP residues 381-740 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE4D / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q08499, 3',5'-cyclic-nucleotide phosphodiesterase #2: Chemical | ChemComp-IHM / #3: Chemical | ChemComp-ZN / #4: 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: 2.65 Å3/Da / Density % sol: 53.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 25%(v/v) ethylene glycol, 10%(v/v) isopropanol, 100mM HEPES, 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: PAL/PLS / Beamline: 6B / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 5, 2005 |
Radiation | Monochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 288261 / Num. obs: 97786 / % possible obs: 94.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.07 / Net I/σ(I): 14.58 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.41 / Num. unique all: 8984 / Rsym value: 0.408 / % possible all: 87.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SL8 Resolution: 2.1→35.41 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 239640.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.546 Å2 / ksol: 0.42 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→35.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Total num. of bins used: 6
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Xplor file |
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