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Yorodumi- PDB-1y2d: Catalytic Domain Of Human Phosphodiesterase 4D In Complex With 1-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y2d | ||||||
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Title | Catalytic Domain Of Human Phosphodiesterase 4D In Complex With 1-(4-methoxy-phenyl)-3,5-dimethyl-1H-pyrazole-4-carboxylic acid ethyl ester | ||||||
Components | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | ||||||
Keywords | HYDROLASE / Phosphodiesterase / PDE / PDE4D / Pyrazole | ||||||
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 / 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 / scaffold protein binding / G alpha (s) signalling events / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Card, G.L. / Blasdel, L. / England, B.P. / Zhang, C. / Suzuki, Y. / Gillette, S. / Fong, D. / Ibrahim, P.N. / Artis, D.R. / Bollag, G. ...Card, G.L. / Blasdel, L. / England, B.P. / Zhang, C. / Suzuki, Y. / Gillette, S. / Fong, D. / Ibrahim, P.N. / Artis, D.R. / Bollag, G. / Milburn, M.V. / Kim, S.-H. / Schlessinger, J. / Zhang, K.Y.J. | ||||||
Citation | Journal: Nat.Biotechnol. / Year: 2005 Title: A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design Authors: Card, G.L. / Blasdel, L. / England, B.P. / Zhang, C. / Suzuki, Y. / Gillette, S. / Fong, D. / Ibrahim, P.N. / Artis, D.R. / Bollag, G. / Milburn, M.V. / Kim, S.-H. / Schlessinger, J. / Zhang, K.Y.J. | ||||||
History |
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Remark 600 | HETEROGEN HOH 1003-1008 ARE ASSOCIATED WITH CHAIN A. HOH 2003-2008 ARE ASSOCIATED WITH CHAIN B. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y2d.cif.gz | 164.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y2d.ent.gz | 126.7 KB | Display | PDB format |
PDBx/mmJSON format | 1y2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y2d_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1y2d_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1y2d_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 1y2d_validation.cif.gz | 46.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/1y2d ftp://data.pdbj.org/pub/pdb/validation_reports/y2/1y2d | HTTPS FTP |
-Related structure data
Related structure data | 1y2bC 1y2cC 1y2eC 1y2hC 1y2jC 1y2kC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 6
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Details | The biological assembly is one monomer. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40096.355 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4D 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)Codon Plus(RIL) References: UniProt: Q08499, 3',5'-cyclic-nucleotide phosphodiesterase |
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-Non-polymers , 6 types, 571 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-B3P / | #7: 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: 2.47 Å3/Da / Density % sol: 50.18 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG3350, ethylene glycol, isopropanol, glycerol and DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→81.65 Å / Num. all: 82929 / Num. obs: 82929 / % possible obs: 99.04 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.7→1.744 Å / Redundancy: 3 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 1.7 / Num. unique all: 6353 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→81.65 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.805 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.092 / ESU R Free: 0.088 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.031 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→81.65 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4973 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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