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Yorodumi- PDB-1xc7: Binding of beta-D-glucopyranosyl bismethoxyphosphoramidate to gly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xc7 | ||||||
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Title | Binding of beta-D-glucopyranosyl bismethoxyphosphoramidate to glycogen phosphorylase b: Kinetic and crystallographic studies | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Chrysina, E.D. / Kosmopoulou, M.N. / Kardakaris, R. / Bischler, N. / Leonidas, D.D. / Kannan, T. / Loganathan, D. / Oikonomakos, N.G. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2005 Title: Binding of beta-d-glucopyranosyl bismethoxyphosphoramidate to glycogen phosphorylase b: kinetic and crystallographic studies Authors: Chrysina, E.D. / Kosmopoulou, M.N. / Kardakaris, R. / Bischler, N. / Leonidas, D.D. / Kannan, T. / Loganathan, D. / Oikonomakos, N.G. #1: Journal: BIOCATAL.BIOTRANSFOR. / Year: 2003 Title: Crystallographic studies on alpha and beta-D-glucopyranosyl formamide analogues, inhibitors of glycogen phosphorylase Authors: Chrysina, E.D. / Oikonomakos, N.G. / Zographos, S.E. / Kosmopoulou, M.N. / Bischler, N. / Leonidas, D. / Kovacs, L. / Docsa, T. / Gergely, P. / Somsak, L. #2: Journal: Eur.J.Biochem. / Year: 2002 Title: Binding of N-acetyl-N '-beta-D-glucopyranosyl urea and N-benzoyl-N '-beta-D-glucopyranosyl urea to glycogen phosphorylase b: kinetic and crystallographic studies Authors: Oikonomakos, N.G. / Kosmopoulou, M. / Zographos, S.E. / Leonidas, D.D. / Chrysina, E.D. / Somsak, L. / Nagy, V. / Praly, J.P. / Docsa, T. / Toth, B. / Gergely, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xc7.cif.gz | 177.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xc7.ent.gz | 143.2 KB | Display | PDB format |
PDBx/mmJSON format | 1xc7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/1xc7 ftp://data.pdbj.org/pub/pdb/validation_reports/xc/1xc7 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 on special symmetry positions |
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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-GL6 / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-PLP / |
#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: 2.79 Å3/Da / Density % sol: 55.51 % |
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 6.8 / Details: pH 6.8, SMALL TUBES, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 7, 2003 / Details: mirrors |
Radiation | Monochromator: Daresbury / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→30 Å / Num. all: 84865 / Num. obs: 84865 / % possible obs: 98.3 % / Observed criterion σ(F): 1.83 / Observed criterion σ(I): 1.83 / Redundancy: 7.3 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.83→1.86 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4137 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→29.36 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3256777.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.8336 Å2 / ksol: 0.332471 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.83→29.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.94 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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