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- PDB-4mi9: Crystal structure of Gpb in complex with SUGAR (N-[(3R)-3-(4-ETHY... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mi9 | ||||||
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Title | Crystal structure of Gpb in complex with SUGAR (N-[(3R)-3-(4-ETHYLPHENYL)BUTANOYL]-BETA-D-GLUCOPYRANOSYLAMINE) (S20) | ||||||
![]() | Glycogen phosphorylase, muscle form | ||||||
![]() | transferase/transferase inhibitor / alpha and beta protein / 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 | ![]() ![]() ![]() | ||||||
![]() | Kantsadi, A.L. / Chatzileontiadou, D.S.M. / Leonidas, D.D. | ||||||
![]() | ![]() Title: Structure based inhibitor design targeting glycogen phosphorylase b. Virtual screening, synthesis, biochemical and biological assessment of novel N-acyl-beta-d-glucopyranosylamines. Authors: Parmenopoulou, V. / Kantsadi, A.L. / Tsirkone, V.G. / Chatzileontiadou, D.S. / Manta, S. / Zographos, S.E. / Molfeta, C. / Archontis, G. / Agius, L. / Hayes, J.M. / Leonidas, D.D. / Komiotis, 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 | ![]() | 185.9 KB | Display | ![]() |
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PDB format | ![]() | 143.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 685 KB | Display | ![]() |
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Full document | ![]() | 689.2 KB | Display | |
Data in XML | ![]() | 31.2 KB | Display | |
Data in CIF | ![]() | 45.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mhoC ![]() 4mhsC ![]() 4mi3C ![]() 4mi6C ![]() 4micC ![]() 3symS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 95509.031 Da / Num. of mol.: 1 / Fragment: unp residues 13-837 / Source method: isolated from a natural source / Details: muscle / Source: (natural) ![]() ![]() |
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#2: Sugar | ChemComp-26W / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.4 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: 10mM BES buffer, pH 6.7, SMALL TUBES, temperature 289K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 21, 2013 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→23.82 Å / Num. all: 82325 / Num. obs: 82325 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rsym value: 0.056 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 11899 / Rsym value: 0.414 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3SYM Resolution: 1.85→23.58 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.55 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.108 / 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: 32.917 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→23.58 Å
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Refine LS restraints |
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