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- PDB-3ms7: Glycogen phosphorylase complexed with 2-chlorobenzaldehyde-4-(2,3... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ms7 | |||||||||
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Title | Glycogen phosphorylase complexed with 2-chlorobenzaldehyde-4-(2,3,4,6-tetra-O-acetyl-beta-D-glucopyranosyl) thiosemicarbazone | |||||||||
![]() | 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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.3 KB | Display | ![]() |
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PDB format | ![]() | 142.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 31.6 KB | Display | |
Data in CIF | ![]() | 45.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mqfC ![]() 3mrtC ![]() 3mrvC ![]() 3mrxC ![]() 3ms2C ![]() 3ms4C ![]() 3mscC ![]() 3mt7C ![]() 3mt8C ![]() 3mt9C ![]() 3mtaC ![]() 3mtbC ![]() 3mtdC ![]() 3nc4C ![]() 2prjS C: citing same article ( S: Starting model for refinement |
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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: 97519.320 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: 2.47 Å3/Da / Density % sol: 50.3 % |
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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 and 3 mM DTT. 20mM inhibitor in 20% DMSO soaked with T-state native enzyme crystal for 11. ...Details: Crystals grown from 20 mg/ml of protein in a buffer solution containing 10 mM BES pH 6.7, 1 mM EDTA and 3 mM DTT. 20mM inhibitor in 20% DMSO soaked with T-state native enzyme crystal for 11.5 hrs, SMALL TUBES, temperature 289K |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2008 |
Radiation | Monochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 71273 / Num. obs: 71273 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.35 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 3 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.14 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PRJ Resolution: 1.95→29.53 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.41 / SU ML: 0.097 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.137 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.285 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→29.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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