+Open data
-Basic information
Entry | Database: PDB / ID: 1zkn | |||||||||
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Title | Structure of PDE4D2-IBMX | |||||||||
Components | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | |||||||||
Keywords | HYDROLASE / PROTEIN-INHIBITOR COMPLEX / INHIBITOR SELECTIVITY | |||||||||
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 | Huai, Q. / Liu, Y. / Francis, S.H. / Corbin, J.D. / Ke, H. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal Structures of Phosphodiesterases 4 and 5 in Complex with Inhibitor 3-Isobutyl-1-Methylxanthine Suggest a Conformation Determinant of Inhibitor Selectivity Authors: Huai, Q. / Liu, Y. / Francis, S.H. / Corbin, J.D. / Ke, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zkn.cif.gz | 270.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zkn.ent.gz | 219.4 KB | Display | PDB format |
PDBx/mmJSON format | 1zkn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/1zkn ftp://data.pdbj.org/pub/pdb/validation_reports/zk/1zkn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38506.727 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE4D / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q08499, 3',5'-cyclic-nucleotide phosphodiesterase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-IBM / #5: 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: 2.88 Å3/Da / Density % sol: 57.31 % |
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Crystal grow | pH: 7.5 / Details: pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 8, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 94246 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Rsym value: 0.074 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.1→2.2 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.44 / % possible all: 64.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDE4D2 CATALYTIC DOMAIN Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 32.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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