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Yorodumi- PDB-1c8l: SYNERGISTIC INHIBITION OF GLYCOGEN PHOSPHORYLASE A BY A POTENTIAL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c8l | ||||||
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Title | SYNERGISTIC INHIBITION OF GLYCOGEN PHOSPHORYLASE A BY A POTENTIAL ANTIDIABETIC DRUG AND CAFFEINE | ||||||
Components | PROTEIN (GLYCOGEN PHOSPHORYLASE) | ||||||
Keywords | TRANSFERASE / GLYCOGEN METABOLISM / DIABETES / PHOSPHORYLASE A / SYNERGISTIC INHIBITION / ALLOSTERIC SITE / INHIBITOR SITE | ||||||
Function / homology | Function and homology information glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å | ||||||
Authors | Tsitsanou, K.E. / Skamnaki, V.T. / Oikonomakos, N.G. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2000 Title: Structural basis of the synergistic inhibition of glycogen phosphorylase a by caffeine and a potential antidiabetic drug. Authors: Tsitsanou, K.E. / Skamnaki, V.T. / Oikonomakos, N.G. #1: Journal: Protein Sci. / Year: 1999 Title: Allosteric Inhibition of Glycogen Phosphorylase a by the Potential Antidiabetic Drug 3-Isopropyl 4-(2-Chlorophenyl)-1,4-Dihydro-1-Ethyl-2-Methyl-Pyridine-3,5,6-Tricarboxylate Authors: Oikonomakos, N.G. / Tsitsanou, K.E. / Zographos, S.E. / Skamnaki, V.T. / Goldmann, S. / Bischoff, H. #2: Journal: Structure / Year: 1997 Title: The Structure of Glycogen Phosphorylase B with an Alkyl-Dihydropyridine-Dicarboxylic Acid Compound, a Novel and Potent Inhibitor Authors: Zographos, S.E. / Oikonomakos, N.G. / Tsitsanou, K.E. / Leonidas, D.D. / Chrysina, E.D. / Skamnaki, V.T. / Bischoff, H. / Goldmann, S. / Watson, K.A. / Johnson, L.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c8l.cif.gz | 195.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c8l.ent.gz | 151.3 KB | Display | PDB format |
PDBx/mmJSON format | 1c8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/1c8l ftp://data.pdbj.org/pub/pdb/validation_reports/c8/1c8l | HTTPS FTP |
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-Related structure data
Related structure data | 3amvS 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: 97371.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLESkeletal muscle / References: UniProt: P00489, glycogen phosphorylase |
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-Non-polymers , 5 types, 708 molecules
#2: Chemical | ChemComp-PLP / |
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#3: Chemical | ChemComp-BIN / |
#4: Chemical | ChemComp-CFF / |
#5: Chemical | ChemComp-GOL / |
#6: 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: 2.37 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.7 / Details: pH 6.70 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.928 |
Detector | Detector: IMAGE PLATE / Date: Apr 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→26.5 Å / Num. obs: 41698 / % possible obs: 98.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.6 / % possible all: 98.5 |
Reflection | *PLUS Num. measured all: 183590 |
Reflection shell | *PLUS % possible obs: 98.5 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: 3AMV Resolution: 2.3→26.5 Å / Cross valid method: R FREE / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.3→26.5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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