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Yorodumi- PDB-3g2i: Crystal structure of 1-(beta-D-glucopyranosyl)-4-substituted-1,2,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g2i | ||||||
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Title | Crystal structure of 1-(beta-D-glucopyranosyl)-4-substituted-1,2,3-triazole | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE / Glycogen phosphorylase / amide-1 / 2 / 3-triazole bioisosterism / Acetylation / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphoprotein / Pyridoxal phosphate | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
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. | ||||||
Citation | Journal: Tetrahedron: Asymmetry / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g2i.cif.gz | 181 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g2i.ent.gz | 141.2 KB | Display | PDB format |
PDBx/mmJSON format | 3g2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/3g2i ftp://data.pdbj.org/pub/pdb/validation_reports/g2/3g2i | HTTPS FTP |
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-Related structure data
Related structure data | 3g2hC 3g2jC 3g2kC 3g2lC 3g2nC 2prjS C: citing same article (ref.) 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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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) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase |
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#2: Sugar | ChemComp-RUG / |
#3: 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: 2.39 Å3/Da / Density % sol: 48.5 % |
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Crystal grow | Temperature: 292 K / Method: small tubes / pH: 6.8 / Details: pH 6.8, SMALL TUBES, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.801 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 20, 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: 1.97→30 Å / Num. obs: 62955 / % possible obs: 98 % / Redundancy: 5.5 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.97→2.08 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3049 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PRJ Resolution: 2→25.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.932 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.157 / 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: 31.262 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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