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Yorodumi- PDB-3cuu: Crystal structure of glycogen phosphorylase b in complex with N-(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cuu | ||||||
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Title | Crystal structure of glycogen phosphorylase b in complex with N-(-D-glucopyranosyl)-N'-(2-naphthyl)oxamides | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE / glycogen phosphorylase / catalytic site / rational inhibitor design / 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 / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Kyritsi, C. / Chrysina, E.D. / Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G. | ||||||
Citation | Journal: To be Published Title: Tracking structure activity relationships of glycogen phosphorylase inhibitors: synthesis, kinetic and crystallographic evaluation of analogues of N-(-D-glucopyranosyl)-N'-oxamides Authors: Czifrak, K. / Kyritsi, C. / Felfoldi, N. / Dosca, T. / Gergely, P. / Chrysina, E.D. / Siafaka-Kapadai, A. / Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cuu.cif.gz | 180.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cuu.ent.gz | 141 KB | Display | PDB format |
PDBx/mmJSON format | 3cuu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/3cuu ftp://data.pdbj.org/pub/pdb/validation_reports/cu/3cuu | HTTPS FTP |
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-Related structure data
Related structure data | 3cutC 3cuvC 3cuwC 1hlfS 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 / Details: muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase |
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#2: Chemical | ChemComp-376 / |
#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: 2.44 Å3/Da / Density % sol: 49.68 % |
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Crystal grow | Temperature: 287 K / Method: small tubes / pH: 6.7 / Details: BES, EDTA, pH6.7, SMALL TUBES, temperature 287K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.04498 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2007 |
Radiation | Monochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04498 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35.7 Å / Num. all: 42548 / Num. obs: 42548 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 33.4 Å2 / Rsym value: 0.095 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.8 / Rsym value: 0.225 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1HLF Resolution: 2.3→32.06 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.81 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.312 / ESU R Free: 0.212 / 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: 32.596 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→32.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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