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- PDB-3g2h: Crystal structure of 1-(beta-D-glucopyranosyl)-4-substituted-1,2,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3g2h | ||||||
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Title | Crystal structure of 1-(beta-D-glucopyranosyl)-4-substituted-1,2,3-triazoles in complex with glycogen phosphorylase | ||||||
![]() | Glycogen phosphorylase, muscle form | ||||||
![]() | TRANSFERASE / Glycogen phosphorylase / amide-1 / 2 / 3-triazole bioisosterism / Acetylation / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphoprotein / Pyridoxal phosphate | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Chrysina, E.D. / Bokor, E. / Alexacou, K.-M. / Charavgi, M.-D. / Oikonomakos, G.N. / Zographos, S.E. / Leonidas, D.D. / Oikonomakos, N.G. / Somsak, L. | ||||||
![]() | ![]() Title: Amide-1,2,3-triazole bioisosterism: the glycogen phosphorylase case Authors: Chrysina, E.D. / Bokor, E. / Alexacou, K.-M. / Charavgi, M.-D. / Oikonomakos, G.N. / Zographos, S.E. / Leonidas, D.D. / Oikonomakos, N.G. / Somsak, L. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Glucose analogue inhibitors of glycogen phosphorylase: from crystallographic analysis to drug prediction using GRID force-field and GOLPE variable selection. Authors: Watson, K.A. / Mitchell, E.P. / Johnson, L.N. / Cruciani, G. / Son, J.C. / Bichard, C.J. / Fleet, G.W. / Oikonomakos, N.G. / Kontou, M. / Zographos, S.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.4 KB | Display | ![]() |
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PDB format | ![]() | 140.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 31.1 KB | Display | |
Data in CIF | ![]() | 43.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3g2iC ![]() 3g2jC ![]() 3g2kC ![]() 3g2lC ![]() 3g2nC ![]() 2prjS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 97519.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Sugar | ChemComp-KOT / |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-IMP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.77 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.8 / Details: pH 6.8, SMALL TUBES, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 21, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.801 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→30 Å / Num. obs: 60007 / % possible obs: 96.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.03→2.06 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 4.3 / Num. unique all: 2991 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2PRJ Resolution: 2.03→29.83 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.784 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.272 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→29.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.082 Å / Total num. of bins used: 20
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