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Yorodumi- PDB-3nc4: The binding of beta-D-glucopyranosyl-thiosemicarbazone derivative... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nc4 | ||||||
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Title | The binding of beta-D-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: a new class of inhibitors | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Glycogenolysis / type 2 diabetes / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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: 2.07 Å | ||||||
Authors | Alexacou, K.-M. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2010 Title: The binding of beta-D-glucopyranosyl-thiosemicarbazone derivatives to glycogen phosphorylase: a new class of inhibitors Authors: Alexacou, K.M. / Tenchiu Deleanu, A.C. / Chrysina, E.D. / Charavgi, M.D. / Kostas, I.D. / Zographos, S.E. / Oikonomakos, N.G. / Leonidas, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nc4.cif.gz | 182.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nc4.ent.gz | 142.5 KB | Display | PDB format |
PDBx/mmJSON format | 3nc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/3nc4 ftp://data.pdbj.org/pub/pdb/validation_reports/nc/3nc4 | HTTPS FTP |
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-Related structure data
Related structure data | 3mqfC 3mrtC 3mrvC 3mrxC 3ms2C 3ms4C 3ms7C 3mscC 3mt7C 3mt8C 3mt9C 3mtaC 3mtbC 3mtdC 2prjS 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: 97432.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / Strain: Rabbit / References: UniProt: P00489, glycogen phosphorylase | ||
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#2: Sugar | #3: 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: 2.45 Å3/Da / Density % sol: 49.89 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: Crystals grown from 20 mg/ml of protein in a buffer solution containing 10 mM BES pH 6.7, 1 mM EDTA, 3 mM DTT. Crystals were soaked with 20mM inhibitor in 20% DMSO for 21 hrs 10 mins, pH 6. ...Details: Crystals grown from 20 mg/ml of protein in a buffer solution containing 10 mM BES pH 6.7, 1 mM EDTA, 3 mM DTT. Crystals were soaked with 20mM inhibitor in 20% DMSO for 21 hrs 10 mins, 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: X13 / Wavelength: 0.815 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2009 |
Radiation | Monochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.815 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→30 Å / Num. all: 48018 / Num. obs: 48018 / % possible obs: 80.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.59 |
Reflection shell | Resolution: 2.07→2.11 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.72 / % possible all: 83.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2PRJ Resolution: 2.07→27.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.109 / SU ML: 0.113 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.638 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→27.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.119 Å / Total num. of bins used: 20
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