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- PDB-3nc4: The binding of beta-D-glucopyranosyl-thiosemicarbazone derivative... -
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Open data
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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 | ||||||
![]() | Glycogen phosphorylase, muscle form | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Glycogenolysis / type 2 diabetes / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Alexacou, K.-M. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.9 KB | Display | ![]() |
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PDB format | ![]() | 142.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 970.3 KB | Display | ![]() |
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Full document | ![]() | 976.6 KB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 45.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ( |
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Similar structure data |
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Links
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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) ![]() ![]() | ||
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#2: Sugar | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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