+Open data
-Basic information
Entry | Database: PDB / ID: 4y62 | ||||||
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Title | AAGlyB in complex with amino-acid analogues | ||||||
Components | Histo-blood group ABO system transferase | ||||||
Keywords | TRANSFERASE / AAGlyB / inhibitor | ||||||
Function / homology | Function and homology information fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding ...fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Wang, S. / Cuesta-Seijo, J.A. / Striebeck, A. / Lafont, D. / Palcic, M.M. / Vidal, S. | ||||||
Citation | Journal: Chempluschem / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y62.cif.gz | 144.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y62.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 4y62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/4y62 ftp://data.pdbj.org/pub/pdb/validation_reports/y6/4y62 | HTTPS FTP |
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-Related structure data
Related structure data | 4y63C 4y64C 4kc1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 40946.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Production host: Escherichia coli (E. coli) References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, fucosylgalactoside 3-alpha-galactosyltransferase |
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#2: Chemical | ChemComp-BHE / |
#3: Chemical | ChemComp-48E / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.954 Å |
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: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→42.4 Å / Num. obs: 98740 / % possible obs: 98.3 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.2→1.4 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 2.56 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KC1 Resolution: 1.6→42.28 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.577 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04 / 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: 15.76 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→42.28 Å
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Refine LS restraints |
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