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Yorodumi- PDB-1gg8: DESIGN OF INHIBITORS OF GLYCOGEN PHOSPHORYLASE: A STUDY OF ALPHA-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gg8 | ||||||
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Title | DESIGN OF INHIBITORS OF GLYCOGEN PHOSPHORYLASE: A STUDY OF ALPHA-AND BETA-C-GLUCOSIDES AND 1-THIO-BETA-D-GLUCOSE COMPOUNDS | ||||||
Components | PROTEIN (GLYCOGEN PHOSPHORYLASE) | ||||||
Keywords | TRANSFERASE / GLYCOGEN PHOSPHORYLASE / INHIBITOR COMPLEX / CATALYTIC SITE / DESIGN | ||||||
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 / OTHER / Resolution: 2.31 Å | ||||||
Authors | Watson, K.A. / Mitchell, E.P. / Johnson, L.N. / Son, J.C. / Bichard, C.J. / Orchard, M.G. / Fleet, G.W. / Oikonomakos, N.G. / Leonidas, D.D. / Kontou, M. / Papageorgiou, A.C. | ||||||
Citation | Journal: Biochemistry / Year: 1994 Title: Design of inhibitors of glycogen phosphorylase: a study of alpha- and beta-C-glucosides and 1-thio-beta-D-glucose compounds. Authors: Watson, K.A. / Mitchell, E.P. / Johnson, L.N. / Son, J.C. / Bichard, C.J. / Orchard, M.G. / Fleet, G.W. / Oikonomakos, N.G. / Leonidas, D.D. / Kontou, M. / Papageorgioui, A. #1: Journal: Protein Sci. / Year: 1995 Title: N-Acetyl-Beta-D-Glucopyranosylamine: A Potent T-State Inhibitor of Glycogen Phosphorylase. A Comparison with Alpha-D-Glucose Authors: Oikonomakos, N.G. / Kontou, M. / Zographos, S.E. / Watson, K.A. / Johnson, L.N. / Bichard, C.J. / Fleet, G.W. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gg8.cif.gz | 185.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gg8.ent.gz | 145 KB | Display | PDB format |
PDBx/mmJSON format | 1gg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/1gg8 ftp://data.pdbj.org/pub/pdb/validation_reports/gg/1gg8 | HTTPS FTP |
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-Related structure data
Related structure data | 2prjS 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
#1: Protein | Mass: 97291.203 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-GLG / |
#3: Chemical | ChemComp-PLP / |
#4: Chemical | ChemComp-IMP / |
#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: 2.47 Å3/Da / Density % sol: 48 % |
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Crystal grow | pH: 6.7 Details: T-STATE GPB CRYSTALS (OIKONOMAKOS ET AL., 1985, BBA 832, 248) WERE SOAKED FOR 1 H IN A BUFFERED SOLUTION [10 MM BES, 0.1 MM EDTA, PH 6.7] CONTAINING A 100 MM CONCENTRATION OF THE COMPOUND. , pH 6.70 |
Crystal grow | *PLUS Method: otherDetails: Oikonomakos, N.G., (1985) Biochim. Biophys. Acta, 832, 248. |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: NICOLET / Detector: AREA DETECTOR / Date: Aug 9, 1993 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→18.5 Å / Num. obs: 34397 / % possible obs: 79.6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.31→2.42 Å |
Reflection | *PLUS Num. measured all: 85299 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: 2PRJ Resolution: 2.31→18.5 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.31→18.5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 18.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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