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Yorodumi- PDB-1hlf: BINDING OF GLUCOPYRANOSYLIDENE-SPIRO-THIOHYDANTOIN TO GLYCOGEN PH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hlf | ||||||
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Title | BINDING OF GLUCOPYRANOSYLIDENE-SPIRO-THIOHYDANTOIN TO GLYCOGEN PHOSPHORYLASE B: KINETIC AND CRYSTALLOGRAPHIC STUD | ||||||
Components | GLYCOGEN PHOSPHORYLASE | ||||||
Keywords | TRANSFERASE / GLYCOGEN PHOSPHORYLASE / INHIBITOR COMPLEX / CATALYTIC SITE / DESIGN | ||||||
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 / OTHER / Resolution: 2.26 Å | ||||||
Authors | Oikonomakos, N.G. / Skamnaki, V.T. / Docsa, T. / Toth, B. / Gergely, P. / Osz, E. / Szilagyi, L. / Somsak, L. | ||||||
Citation | Journal: BIOORG.MED.CHEM. / Year: 2002 Title: Kinetic and crystallographic studies of glucopyranosylidene spirothiohydantoin binding to glycogen phosphorylase B Authors: Oikonomakos, N.G. / Skamnaki, V.T. / Osz, E. / Szilagyi, L. / Somsak, L. / Docsa, T. / Toth, B. / Gergely, P. #1: Journal: Tetrahedron Lett. / Year: 1995 Title: Potent Inhibition of Glycogen Phosphorylase by a Spirohydantoin of Glucopyranose: First Pyranose Analogues of Hydantocidin Authors: Bichard, C.J. / Mitchell, E.P. / Wormald, M.R. / Watson, K.A. / Johnson, L.N. / Zographos, S.E. / Koutra, D.D. / Oikonomakos, N.G. / Fleet, G.W. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hlf.cif.gz | 183.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hlf.ent.gz | 144.5 KB | Display | PDB format |
PDBx/mmJSON format | 1hlf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/1hlf ftp://data.pdbj.org/pub/pdb/validation_reports/hl/1hlf | HTTPS FTP |
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-Related structure data
Related structure data | 1ggnC 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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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: Chemical | ChemComp-PLP / |
#3: Sugar | ChemComp-GL4 / ( |
#4: 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: small tubes / pH: 6.7 Details: CRYSTALLIZATION CONDITIONS: T-STATE GPB CRYSTALS (OIKONOMAKOS ET AL., 1985, BBA 832, 248) WERE SOAKED FOR 1 H IN A BUFFERED SOLUTION [10 MM BES, 0.1 MM EDTA, PH 6.7] CONTAINING A 70 MM ...Details: CRYSTALLIZATION CONDITIONS: T-STATE GPB CRYSTALS (OIKONOMAKOS ET AL., 1985, BBA 832, 248) WERE SOAKED FOR 1 H IN A BUFFERED SOLUTION [10 MM BES, 0.1 MM EDTA, PH 6.7] CONTAINING A 70 MM CONCENTRATION OF THE COMPOUND, pH 6.70, SMALL TUBES, temperature 289K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: unknownDetails: Oikonomakos, N.G., (1985) Biochim.Biophys.Acta., 832, 248. | ||||||||||||||||||||||||||||||
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: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 18, 1996 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→28.06 Å / Num. obs: 45104 / % possible obs: 97.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.041 |
Reflection shell | Resolution: 2.26→2.3 Å / Rmerge(I) obs: 0.158 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 255617 |
Reflection shell | *PLUS % possible obs: 99.9 % / Mean I/σ(I) obs: 5.5 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: 2PRJ Resolution: 2.26→28.06 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→28.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.26→28.06 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.221 / Rfactor Rwork: 0.193 |