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Yorodumi- PDB-3o56: Catalytic domain of human phosphodiesterase 4b2b in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 3o56 | ||||||
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Title | Catalytic domain of human phosphodiesterase 4b2b in complex with a 5-heterocycle pyrazolopyridine inhibitor | ||||||
Components | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / PDE / HYDROLASE / PHOSPHODIESTERASE / cAMP Binding / 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.42 Å | ||||||
Authors | Somers, D.O. / Neu, M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Pyrazolopyridines as potent PDE4B inhibitors: 5-heterocycle SAR. Authors: Mitchell, C.J. / Ballantine, S.P. / Coe, D.M. / Cook, C.M. / Delves, C.J. / Dowle, M.D. / Edlin, C.D. / Hamblin, J.N. / Holman, S. / Johnson, M.R. / Jones, P.S. / Keeling, S.E. / Kranz, M. / ...Authors: Mitchell, C.J. / Ballantine, S.P. / Coe, D.M. / Cook, C.M. / Delves, C.J. / Dowle, M.D. / Edlin, C.D. / Hamblin, J.N. / Holman, S. / Johnson, M.R. / Jones, P.S. / Keeling, S.E. / Kranz, M. / Lindvall, M. / Lucas, F.S. / Neu, M. / Solanke, Y.E. / Somers, D.O. / Trivedi, N.A. / Wiseman, J.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o56.cif.gz | 87.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o56.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 3o56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/3o56 ftp://data.pdbj.org/pub/pdb/validation_reports/o5/3o56 | HTTPS FTP |
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-Related structure data
Related structure data | 3o57C 3d3pS S: Starting model for refinement C: citing same article (ref.) |
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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: 40583.949 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP residues 324-675 / Mutation: S482A, S487A, S489A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE4B, DPDE4 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q07343, 3',5'-cyclic-nucleotide phosphodiesterase |
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-Non-polymers , 6 types, 132 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-MG / | ||||||
#4: Chemical | #5: Chemical | ChemComp-ZG1 / | #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: 2.71 Å3/Da / Density % sol: 54.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 14-18% PEG 3000, 10% Glycerol, 50mM Sodium Cacodylate pH 6.5, 100mM Sodium Acetate, 1M Sodium Chloride, 1% DMF, 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.42→29.703 Å / Num. obs: 17117 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 52.5 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 16.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3D3P Resolution: 2.42→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2592 / WRfactor Rwork: 0.2008 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7846 / SU B: 9.207 / SU ML: 0.211 / SU R Cruickshank DPI: 0.38 / SU Rfree: 0.2703 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.61 Å2 / Biso mean: 57.0208 Å2 / Biso min: 9.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.42→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.42→2.482 Å / Total num. of bins used: 20
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