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- PDB-7a8q: Crystal structure of human phosphodiesterase 4D2 catalytic domain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7a8q | ||||||
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Title | Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-654 | ||||||
![]() | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | ||||||
![]() | HYDROLASE / Phosphodiesterase / cAMP hydrolysis / alternative splicing | ||||||
Function / homology | ![]() 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 / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / establishment of endothelial barrier / regulation of cardiac muscle cell contraction / negative regulation of cAMP-mediated signaling / 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 / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / establishment of endothelial barrier / regulation of cardiac muscle cell contraction / negative regulation of cAMP-mediated signaling / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / voltage-gated calcium channel complex / positive regulation of heart rate / heterocyclic compound binding / adrenergic receptor signaling pathway / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-serine phosphorylation / cAMP catabolic process / 3',5'-cyclic-nucleotide phosphodiesterase activity / DARPP-32 events / calcium channel regulator activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / beta-2 adrenergic receptor binding / cAMP binding / cellular response to cAMP / calcium channel complex / cellular response to epinephrine stimulus / positive regulation of interleukin-2 production / regulation of heart rate / cAMP-mediated signaling / positive regulation of type II interferon production / T cell receptor signaling pathway / ATPase binding / G alpha (s) signalling events / scaffold protein binding / transmembrane transporter binding / apical plasma membrane / centrosome / perinuclear region of cytoplasm / enzyme binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Singh, A.K. / Blaazer, A.R. / Zara, L. / de Esch, I.J.P. / Leurs, R. / Brown, D.G. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: hPDE4D2 structure with inhibitor NPD-654 Authors: Singh, A.K. / Brown, D.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291.7 KB | Display | ![]() |
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PDB format | ![]() | 235.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 54.8 KB | Display | |
Data in CIF | ![]() | 76.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sl3S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41808.242 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: residues 381-740 / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q08499, 3',5'-cyclic-AMP phosphodiesterase |
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-Non-polymers , 7 types, 514 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/R4H.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/R4H.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-EPE / #6: Chemical | #7: Chemical | ChemComp-PEG / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 24% PEG 3350, 30% Ethylene glycol, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2016 / Details: CRL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→160.22 Å / Num. obs: 85619 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.24→2.25 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.946 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 836 / CC1/2: 0.72 / Rpim(I) all: 0.391 / Rrim(I) all: 1.025 / % possible all: 98.4 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3SL3 Resolution: 2.24→91.49 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.487 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.196 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 177.27 Å2 / Biso mean: 54.493 Å2 / Biso min: 26.11 Å2
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Refinement step | Cycle: final / Resolution: 2.24→91.49 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.245→2.303 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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