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- PDB-1k08: Crystallographic Binding Study of 10 mM N-benzoyl-N'-beta-D-gluco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k08 | ||||||
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Title | Crystallographic Binding Study of 10 mM N-benzoyl-N'-beta-D-glucopyranosyl urea to glycogen phosphorylase b | ||||||
![]() | Glycogen Phosphorylase | ||||||
![]() | TRANSFERASE / glycogen phosphorylase / catalytic site / new allosteric site | ||||||
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 | ![]() ![]() | ||||||
![]() | Oikonomakos, N.G. / Kosmopoulou, M. / Zographos, S.E. / Leonidas, D.D. / Chrysina, E.D. / Somsak, L. / Nagy, V. / Praly, J.P. / Docsa, T. / Toth, B. / Gergely, P. | ||||||
![]() | ![]() Title: Binding of N-acetyl-N '-beta-D-glucopyranosyl urea and N-benzoyl-N '-beta-D-glucopyranosyl urea to glycogen phosphorylase b: kinetic and crystallographic studies. Authors: Oikonomakos, N.G. / Kosmopoulou, M. / Zographos, S.E. / Leonidas, D.D. / Chrysina, E.D. / Somsak, L. / Nagy, V. / Praly, J.P. / Docsa, T. / Toth, B. / Gergely, P. #1: ![]() Title: A New Allosteric Site in Glycogen Phosphorylase B as a Target for Drug Interactions Authors: Oikonomakos, N.G. / Skamnaki, V.T. / Tsitsanou, K.E. / Gavalas, N.G. / Johnson, L.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.2 KB | Display | ![]() |
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PDB format | ![]() | 143.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1k06C ![]() 1ktiC ![]() 1hlfS 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: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
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#2: Sugar | #3: Chemical | ChemComp-PLP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.23 % |
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Crystal grow | Temperature: 287 K / Method: small tubes / pH: 6.7 Details: BES, EDTA, 10mM N-benzoyl-N'-beta-D-glucopyranosyl urea, pH 6.7, SMALL TUBES, temperature 287K |
Crystal grow | *PLUS Details: Oikonomakos, N.G., (1985) Biochim. Biophys. Acta, 832, 248. |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 2, 2001 / Details: mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→28.75 Å / Num. all: 44261 / Num. obs: 44361 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 28 Å2 / Rsym value: 9.6 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.26→2.3 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1976 / Rsym value: 42.4 / % possible all: 86.5 |
Reflection | *PLUS Num. measured all: 391254 / Rmerge(I) obs: 0.096 |
Reflection shell | *PLUS % possible obs: 86.5 % / Rmerge(I) obs: 0.424 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HLF Resolution: 2.26→28.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.26→28.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.26→2.4 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Software | *PLUS Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.336 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.304 |