[English] 日本語
Yorodumi- PDB-2ff5: Synthesis of C-D-Glycopyranosyl-Hydroquinones and-Benzoquinones. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ff5 | ||||||
---|---|---|---|---|---|---|---|
Title | Synthesis of C-D-Glycopyranosyl-Hydroquinones and-Benzoquinones. Inhibition of PTP1B. Inhibition of and binding to glycogen phosphorylase in the crystal | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE / glycogenolysis / type 2 diabetes | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.03 Å | ||||||
Authors | Chrysina, E.D. / Kosmopoulou, M.N. / Leonidas, D.D. / Oikonomakos, N.G. | ||||||
Citation | Journal: Eur.J.Org.Chem. / Year: 2007 Title: In the Search of Glycogen Phosphorylase Inhibitors: Synthesis of C-D-Glycopyranosylbenzo(hydro)quinones Inhibition of and Binding to Glycogen Phosphorylase in the Crystal Authors: He, L. / Zhang, Y.Z. / Tanoh, M. / Chen, G.-R. / Praly, J.-P. / Chrysina, E.D. / Tiraidis, C. / Kosmopoulou, M. / Leonidas, D.D. / Oikonomakos, N.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ff5.cif.gz | 178.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ff5.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ff5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/2ff5 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/2ff5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2prjS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | Dimeric glycogen phosphorylase is the physiologically active species |
-Components
#1: Protein | Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PYRIDOXAL-5'-PHOSPHATE bound / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MuscleSkeletal muscle / References: UniProt: P00489, glycogen phosphorylase |
---|---|
#2: Chemical | ChemComp-PLP / |
#3: Sugar | ChemComp-H53 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.66 % |
---|---|
Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: 10 mM Bes buffer, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 31, 2003 |
Radiation | Monochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.803 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→21.36 Å / Num. all: 61307 / Num. obs: 61307 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 32.2 Å2 / Rsym value: 0.059 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.03→2.06 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 3029 / Rsym value: 0.532 / % possible all: 98.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2PRJ Resolution: 2.03→21.36 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3470165.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.2686 Å2 / ksol: 0.360333 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.1 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→21.36 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.03→2.16 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|