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Yorodumi- PDB-1lwo: Crystal structure of rabbit muscle glycogen phosphorylase a in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lwo | ||||||
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Title | Crystal structure of rabbit muscle glycogen phosphorylase a in complex with a potential hypoglycaemic drug at 2.0 A resolution | ||||||
Components | glycogen phosphorylase | ||||||
Keywords | TRANSFERASE / type 2 diabetes / glycogen phosphorylase / inhibitor / new allosteric site | ||||||
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 Å | ||||||
Authors | Oikonomakos, N.G. / Chrysina, E.D. / Kosmopoulou, M.N. / Leonidas, D.D. | ||||||
Citation | Journal: BIOCHEM.BIOPHYS.ACTA PROTEINS & PROTEOMICS / Year: 2003 Title: Crystal structure of rabbit muscle glycogen phosphorylase a in complex with a potential hypoglycaemic drug at 2.0 A resolution Authors: Oikonomakos, N.G. / Chrysina, E.D. / Kosmopoulou, M.N. / Leonidas, D.D. #1: Journal: BIOORG.MED.CHEM. / Year: 2002 Title: The 1.76 A Resolution Crystal Structure of Glycogen Phosphorylase b Complexed with Glucose, and CP320626, a Potential Antidiabetic Drug Authors: Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Archontis, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lwo.cif.gz | 185.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lwo.ent.gz | 144 KB | Display | PDB format |
PDBx/mmJSON format | 1lwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/1lwo ftp://data.pdbj.org/pub/pdb/validation_reports/lw/1lwo | HTTPS FTP |
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-Related structure data
Related structure data | 1lwnSC S: Starting model for refinement C: citing same article (ref.) |
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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: 97371.180 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-GLC / |
#3: Chemical | ChemComp-PLP / |
#4: Chemical | ChemComp-CHI / |
#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: 50.3 % |
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 6.7 / Details: BES, EDTA, pH 6.7, SMALL TUBES, temperature 298K |
Crystal grow | *PLUS Details: Oikonomakos, N.G., (1999) Protein Sci., 8, 1930. |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.05 Å |
Detector | Detector: IMAGE PLATE / Date: Mar 3, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 67901 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3121 / % possible all: 95.7 |
Reflection | *PLUS Num. obs: 64780 / Num. measured all: 343075 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 95.7 % / Num. unique obs: 3121 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1LWN Resolution: 2→29.36 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 29.4 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.315 / Rfactor obs: 0.307 |