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Yorodumi- PDB-4myq: Selective Inhibition of the Catalytic Domain Of Human Phosphodies... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4myq | ||||||
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Title | Selective Inhibition of the Catalytic Domain Of Human Phosphodiesterase 4B With A-33 | ||||||
Components | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / PHOSPHODIESTERASE / CATALYTIC / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / gamma-tubulin complex / negative regulation of relaxation of cardiac muscle / 3',5'-cyclic-AMP phosphodiesterase / neutrophil homeostasis / gamma-tubulin binding / regulation of cardiac muscle cell contraction / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / voltage-gated calcium channel complex / leukocyte migration ...negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / gamma-tubulin complex / negative regulation of relaxation of cardiac muscle / 3',5'-cyclic-AMP phosphodiesterase / neutrophil homeostasis / gamma-tubulin binding / regulation of cardiac muscle cell contraction / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / voltage-gated calcium channel complex / leukocyte migration / cAMP catabolic process / excitatory synapse / DARPP-32 events / calcium channel regulator activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP binding / cellular response to epinephrine stimulus / positive regulation of interleukin-2 production / cAMP-mediated signaling / neutrophil chemotaxis / Z disc / positive regulation of type II interferon production / synaptic vesicle / cellular response to xenobiotic stimulus / T cell receptor signaling pathway / cellular response to lipopolysaccharide / transmembrane transporter binding / dendritic spine / postsynaptic density / centrosome / perinuclear region of cytoplasm / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Fox III, D. / Edwards, T.E. | ||||||
Citation | Journal: Cell Signal / Year: 2014 Title: Structural basis for the design of selective phosphodiesterase 4B inhibitors. Authors: Fox, D. / Burgin, A.B. / Gurney, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4myq.cif.gz | 96.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4myq.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 4myq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/4myq ftp://data.pdbj.org/pub/pdb/validation_reports/my/4myq | HTTPS FTP |
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-Related structure data
Related structure data | 3g45S 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42813.164 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 324-691 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPDE4, PDE4, PDE4B / Plasmid: PEMB44 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q07343, 3',5'-cyclic-nucleotide phosphodiesterase |
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-Non-polymers , 6 types, 382 molecules
#2: Chemical | ChemComp-19T / ( | ||
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#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-ZN / | ||
#5: Chemical | ChemComp-NA / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.93 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: VCID6271 PDE4 AT 7.9 MG/ML IN 20MM HEPES PH 7.5, 100 MM NACL, 1MM DTT, WITH 0.5MM A-33 AGAINST JCSG_ A10 (OPTIMIZATION SCREEN), 328.57MM POTASSIUM FORMATE, 24% W/V PEG 3350, CRYO 20% ...Details: VCID6271 PDE4 AT 7.9 MG/ML IN 20MM HEPES PH 7.5, 100 MM NACL, 1MM DTT, WITH 0.5MM A-33 AGAINST JCSG_ A10 (OPTIMIZATION SCREEN), 328.57MM POTASSIUM FORMATE, 24% W/V PEG 3350, CRYO 20% ETHYLENE GLYCOL AND 0.1MM COMPOUND, CRYSTAL TRACKING ID 232128E12, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K, temperature 289.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.85 Å / Num. all: 36759 / Num. obs: 35759 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 18.71 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.9→1.95 Å / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.3 / % possible all: 86.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3G45 Resolution: 1.9→49.85 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.908 / SU B: 3.137 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.143 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 12.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→49.85 Å
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