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Yorodumi- PDB-2gpa: ALLOSTERIC INHIBITION OF GLYCOGEN PHOSPHORYLASE A BY A POTENTIAL ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gpa | ||||||
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Title | ALLOSTERIC INHIBITION OF GLYCOGEN PHOSPHORYLASE A BY A POTENTIAL ANTIDIABETIC DRUG | ||||||
Components | PROTEIN (GLYCOGEN PHOSPHORYLASE) | ||||||
Keywords | TRANSFERASE / DIABETES / GLYCOGEN METABOLISM / PHOSPHORYLASE A / INHIBITION / ALLOSTERIC 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 Å | ||||||
Authors | Oikonomakos, N.G. / Tsitsanou, K.E. / Zographos, S.E. / Skamnaki, V.T. | ||||||
Citation | 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-tricarbo xylate. Authors: Oikonomakos, N.G. / Tsitsanou, K.E. / Zographos, S.E. / Skamnaki, V.T. / Goldmann, S. / Bischoff, H. #1: Journal: To be Published 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: 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. / Goldman, S. / Schramm, M. / 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 | 2gpa.cif.gz | 192.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gpa.ent.gz | 152 KB | Display | PDB format |
PDBx/mmJSON format | 2gpa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/2gpa ftp://data.pdbj.org/pub/pdb/validation_reports/gp/2gpa | 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: 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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#2: Sugar | ChemComp-GLC / |
#3: Chemical | ChemComp-PLP / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 2.41 Å3/Da / Density % sol: 48 % |
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Crystal grow | pH: 6.7 / Details: pH 6.7 |
Crystal grow | *PLUS Method: other / Details: Fletterick, R.J., (1976) J. Mol. Biol., 103, 1. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
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→13 Å / Num. obs: 57879 / % possible obs: 90.1 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5 / % possible all: 92.6 |
Reflection | *PLUS Lowest resolution: 13 Å / Num. measured all: 448708 |
Reflection shell | *PLUS % possible obs: 92.6 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2→10 Å / Cross valid method: R FREE / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 0 / Num. reflection Rfree: 2947 / % reflection Rfree: 5 % / Rfactor obs: 0.179 / Rfactor Rfree: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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