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- PDB-5lrd: Crystal structure of Glycogen Phosphorylase b in complex with KS242 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lrd | ||||||
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Title | Crystal structure of Glycogen Phosphorylase b in complex with KS242 | ||||||
![]() | Glycogen phosphorylase, muscle form![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kantsadi, A.L. / Leonidas, D.D. | ||||||
![]() | ![]() Title: van der Waals interactions govern C-beta-d-glucopyranosyl triazoles' nM inhibitory potency in human liver glycogen phosphorylase. Authors: Kantsadi, A.L. / Stravodimos, G.A. / Kyriakis, E. / Chatzileontiadou, D.S.M. / Solovou, T.G.A. / Kun, S. / Bokor, E. / Somsak, L. / 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 | ![]() | 179.4 KB | Display | ![]() |
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PDB format | ![]() | 146.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 539 KB | Display | ![]() |
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Full document | ![]() | 543.1 KB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 97422.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-KS2 / ( | ||
#3: Chemical | ChemComp-PLP / ![]() | ||
#4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.97 % |
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Crystal grow![]() | Temperature: 289 K / Method: small tubes / pH: 6.8 / Details: 10mM BES buffer |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→38.37 Å / Num. obs: 88657 / % possible obs: 98.5 % / Redundancy: 4.6 % / Rsym value: 0.06 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.5 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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: 31.473 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→37.14 Å
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Refine LS restraints |
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