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Yorodumi- PDB-2prj: Binding of N-acetyl-beta-D-glucopyranosylamine to Glycogen Phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2prj | |||||||||
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Title | Binding of N-acetyl-beta-D-glucopyranosylamine to Glycogen Phosphorylase B | |||||||||
Components | GLYCOGEN PHOSPHORYLASE | |||||||||
Keywords | TRANSFERASE / GLYCOGEN PHOSPHORYLASE | |||||||||
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 / Resolution: 2.3 Å | |||||||||
Authors | Oikonomakos, N.G. / Kontou, M. / Zographos, S.E. / Watson, K.A. / Johnson, L.N. / Bichard, C.J.F. / Fleet, G.W.J. / Acharya, K.R. | |||||||||
Citation | Journal: Protein Sci. / Year: 1995 Title: N-acetyl-beta-D-glucopyranosylamine: a potent T-state inhibitor of glycogen phosphorylase. A comparison with alpha-D-glucose. Authors: Oikonomakos, N.G. / Kontou, M. / Zographos, S.E. / Watson, K.A. / Johnson, L.N. / Bichard, C.J. / Fleet, G.W. / Acharya, K.R. #1: Journal: Biochemistry / Year: 1994 Title: The Design of Inhibitors of Glycogen Phosphorylase: A Study of Alpha and Beta Glucoheptonamides and 1-Thio-Beta-D-Glucose Compounds Authors: Watson, K.A. / Mitchell, E.P. / Johnson, L.N. / Son, J.C. / Bichard, C.J.F. / Orchard, M.G. / Fleet, G.W.J. / Oikonomakos, N.G. / Leonidas, D.D. / Kontou, M. / Papageorgiou, A.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2prj.cif.gz | 184.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2prj.ent.gz | 145.2 KB | Display | PDB format |
PDBx/mmJSON format | 2prj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/2prj ftp://data.pdbj.org/pub/pdb/validation_reports/pr/2prj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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-NBG / |
#3: Chemical | ChemComp-PLP / |
#4: Chemical | ChemComp-IMP / |
#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: 2.47 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: GLYCOGEN PHOSPHORYLASE WAS CO-CRYSTALLISED WITH 20 MM N-ACETYL-BETA-D-GLUCOPYRANOSYLAMINE IN A MEDIUM CONSISTING OF 20-30 MG/ML ENZYME, 1 MM IMP, 1 MM SPERMINE, 10 MM BES, 3 MM ...Details: GLYCOGEN PHOSPHORYLASE WAS CO-CRYSTALLISED WITH 20 MM N-ACETYL-BETA-D-GLUCOPYRANOSYLAMINE IN A MEDIUM CONSISTING OF 20-30 MG/ML ENZYME, 1 MM IMP, 1 MM SPERMINE, 10 MM BES, 3 MM DITHIOTHREITOL, 0.1 MM EDTA, 0.02% (W/V) SODIUM AZIDE, PH 6.7 AT 16 C, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Date: Aug 9, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→28.17 Å / Num. obs: 35730 / % possible obs: 81.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.3→2.4 Å / % possible all: 46.5 |
Reflection | *PLUS % possible obs: 84 % / Num. measured all: 62732 |
-Processing
Software |
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Refinement | Resolution: 2.3→18.17 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.3→18.17 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 34607 / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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