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- PDB-3amv: ALLOSTERIC INHIBITION OF GLYCOGEN PHOSPHORYLASE A BY A POTENTIAL ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3amv | ||||||
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Title | ALLOSTERIC INHIBITION OF GLYCOGEN PHOSPHORYLASE A BY A POTENTIAL ANTIDIABETIC DRUG | ||||||
![]() | PROTEIN (GLYCOGEN PHOSPHORYLASE) | ||||||
![]() | TRANSFERASE / DIABETES / GLYCOGEN METABOLISM / PHOSPHORYLASE A / INHIBITION / ALLOSTERIC SITE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Oikonomakos, N.G. / Tsitsanou, K.E. / Zographos, S.E. / Skamnaki, V.T. | ||||||
![]() | ![]() 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-tricarbo xylate. Authors: Oikonomakos, N.G. / Tsitsanou, K.E. / Zographos, S.E. / Skamnaki, V.T. / Goldmann, S. / Bischoff, H. #1: ![]() Title: Effects of Commonly Used Cryoprotectants on Glycogen Phosphorylase Activity and Structure Authors: Tsitsanou, K.E. / Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Gregoriou, M. / Watson, K.A. / Johnson, L.N. / Fleet, G.W.J. #2: ![]() 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. / Goldman, S. / Schramm, M. / Watson, K.A. / Johnson, L.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.4 KB | Display | ![]() |
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PDB format | ![]() | 152.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 512.1 KB | Display | ![]() |
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Full document | ![]() | 531.4 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 32.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/GLC.gif)
![](data/chem/img/GLC.gif)
#1: Protein | Mass: 97371.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Sugar | ChemComp-GLC / |
-Non-polymers , 4 types, 756 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/BIN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BIN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PLP / |
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#4: Chemical | ChemComp-BIN / |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48 % | |||||||||||||||
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Crystal grow | pH: 6.7 Details: 1 MM W1807 IN A MEDIUM CONSISTING OF 20-24 MG/ML ENZYME, 10 MM MAGNESIUM ACETATE, 3 MM DTT, 10 MM BES, 0.1 MM EDTA, AND 0.02% SODIUM AZIDE, PH 6.7 (22 DEG C). | |||||||||||||||
Crystal grow | *PLUS Temperature: 100 K / 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: ![]() ![]() ![]() |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1997 |
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→13 Å / Num. obs: 51612 / % possible obs: 92.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.35 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2.5 / % possible all: 87.3 |
Reflection | *PLUS Num. measured all: 337366 |
Reflection shell | *PLUS % possible obs: 87.3 % |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 2.1→13 Å / Cross valid method: R FREE / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.1→13 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 48964 / Num. reflection Rfree: 2648 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.9 Å2 |