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Open data
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Basic information
Entry | Database: PDB / ID: 4y63 | ||||||
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Title | AAGlyB in complex with amino-acid analogues | ||||||
![]() | Histo-blood group ABO system transferase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, S. / Cuesta-Seijo, J.A. / Striebeck, A. / Lafont, D. / Palcic, M.M. / Vidal, S. | ||||||
![]() | ![]() Title: Design of Glycosyltransferase Inhibitors: Serine Analogues as Pyrophosphate Surrogates? Authors: Wang, S. / Cuesta-Seijo, J.A. / Striebeck, A. / Lafont, D. / Palcic, M.M. / Vidal, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.8 KB | Display | ![]() |
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PDB format | ![]() | 113.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4y62C ![]() 4y64C ![]() 4kc1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 40946.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, ![]() |
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#2: Chemical | ChemComp-BHE / |
#3: Chemical | ChemComp-48O / |
#4: Chemical | ChemComp-MN / |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.17 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350 ammonium sulfate MOPS MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.3→42.3 Å / Num. obs: 77776 / % possible obs: 99.6 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.69 |
Reflection shell | Resolution: 1.3→1.5 Å / Redundancy: 13 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.99 / Num. unique all: 26858 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4KC1 Resolution: 1.3→42.3 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.749 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.046 / 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: 13.826 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→42.3 Å
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Refine LS restraints |
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