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- PDB-1h5u: THE 1.76 A RESOLUTION CRYSTAL STRUCTURE OF GLYCOGEN PHOSPHORYLASE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1h5u | ||||||
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Title | THE 1.76 A RESOLUTION CRYSTAL STRUCTURE OF GLYCOGEN PHOSPHORYLASE B COMPLEXED WITH GLUCOSE AND CP320626, A POTENTIAL ANTIDIABETIC DRUG | ||||||
![]() | GLYCOGEN PHOSPHORYLASE![]() | ||||||
![]() | GLYCOGEN METABOLISM / GLYCOGEN PHOSPHORYLASE B / ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Archontis, G. | ||||||
![]() | ![]() Title: The 1.76 A Resolution Crystal Structure of Glycogen Phosphorylase B Complexed with Glucose, and Cp320626, a Potential Antidiabetic Drug Authors: Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Archontis, G. #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 | ![]() | 185.1 KB | Display | ![]() |
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PDB format | ![]() | 144.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1c50S 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: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CHI / |
#3: Sugar | ChemComp-GLC / ![]() |
#4: Chemical | ChemComp-PLP / ![]() |
#5: Water | ChemComp-HOH / ![]() |
Sequence details | REFERENCE: K.NAKANO, P.K.HWANG, R.J.FLETTERICK, FEBS LETT., V. 204, P. 283, 1986. HIGH RESOLUTION ...REFERENCE: K.NAKANO, P.K.HWANG, R.J.FLETTERICK |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | pH: 6.7 Details: PHOSPHORYLASE B-GLC-CP320626 COMPLEX WAS CO-CRYSTALLISED UNDER CONDITIONS SIMILAR TO THOSE DESCRIBED BY OIKONOMAKOS ET AL., (2000) STRUCTURE 8, 575-584., pH 6.70 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 6.7 / Method: unknownDetails: Zographos, S.E., (1997) Structure (London), 5, 1413. | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Mar 3, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.76→26.25 Å / Num. obs: 93061 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.41 |
Reflection shell | Resolution: 1.76→1.79 Å / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2.33 / % possible all: 94.8 |
Reflection | *PLUS Num. measured all: 483106 |
Reflection shell | *PLUS % possible obs: 94.8 % / Mean I/σ(I) obs: 2.33 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1C50 Resolution: 1.76→26.25 Å / Cross valid method: FREE R-VALUE / σ(F): 0 Details: RESIDUES WHERE B-FACTOR VALUES OF MAIN CHAIN ATOMS EXCEED 60 A2 INCLUDE 13-17, 209-211, 250-254, 260, 313-314, 324-325, 550-557, AND 831-837. THE SAME RESIDUES ARE ALSO POORLY ORDERED IN THE ...Details: RESIDUES WHERE B-FACTOR VALUES OF MAIN CHAIN ATOMS EXCEED 60 A2 INCLUDE 13-17, 209-211, 250-254, 260, 313-314, 324-325, 550-557, AND 831-837. THE SAME RESIDUES ARE ALSO POORLY ORDERED IN THE NATIVE ENZYME STRUCTURE
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Refinement step | Cycle: LAST / Resolution: 1.76→26.25 Å
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Refine LS restraints |
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Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.76 Å / Lowest resolution: 1.79 Å / Rfactor Rfree: 0.366 / Rfactor Rwork: 0.342 |