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Yorodumi- PDB-1kti: BINDING OF 100 MM N-ACETYL-N'-BETA-D-GLUCOPYRANOSYL UREA TO GLYCO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kti | |||||||||
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Title | BINDING OF 100 MM N-ACETYL-N'-BETA-D-GLUCOPYRANOSYL UREA 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 / FOURIER SYNTHESIS / Resolution: 1.97 Å | |||||||||
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. | |||||||||
Citation | 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. #1: 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. #2: Journal: Structure / Year: 2000 Title: A New Allosteric Site in Glycogen Phosphorylase b as a Target for Drug Interactions Authors: Oikonomakos, N.G. / Skamnaki, V.T. / Tsitsanou, K.E. / Gavalas, N.G. / Johnson, L.N. | |||||||||
History |
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Remark 999 | sequence the authors state that according to the electron density map at 1.97 A resolution residue ...sequence the authors state that according to the electron density map at 1.97 A resolution residue 380 is an ILE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kti.cif.gz | 174.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kti.ent.gz | 140.9 KB | Display | PDB format |
PDBx/mmJSON format | 1kti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/1kti ftp://data.pdbj.org/pub/pdb/validation_reports/kt/1kti | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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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 / Details: MUSCLE / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase |
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#2: Sugar | ChemComp-AZC / |
#3: Chemical | ChemComp-PLP / |
#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: 2.46 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: BES, EDTA, 100 MM N-ACETYL-N'-BETA-D-GLUCOPYRANOSYL UREA, pH 6.7, SMALL TUBES, temperature 289K |
-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 | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 2001 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→28.8 Å / Num. obs: 66108 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.048 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.97→2 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 16.7 / Num. unique all: 66108 / Rsym value: 0.048 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.97→28.71 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3470156.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.471 Å2 / ksol: 0.360828 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.97→28.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.09 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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