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Yorodumi- PDB-4kc1: Structure of the blood group glycosyltransferase AAglyB in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kc1 | ||||||
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Title | Structure of the blood group glycosyltransferase AAglyB in complex with a pyridine inhibitor as a neutral pyrophosphate surrogate | ||||||
Components | Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase | ||||||
Keywords | Transferase/Transferase Inhibitor / GTA superfanily / blood group proteins / glycosyltransferase / Fuc-Gal / ADP-Gal / ADP-GalNAc / Transferase-Transferase Inhibitor complex | ||||||
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: 1.5 Å | ||||||
Authors | Cuesta-Seijo, J.A. / Wang, S. / Lafont, D. / Vidal, S. / Palcic, M.M. | ||||||
Citation | Journal: Chemistry / Year: 2013 Title: Design of glycosyltransferase inhibitors: pyridine as a pyrophosphate surrogate. Authors: Wang, S. / Cuesta-Seijo, J.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 | 4kc1.cif.gz | 161.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kc1.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 4kc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kc1_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4kc1_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4kc1_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 4kc1_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/4kc1 ftp://data.pdbj.org/pub/pdb/validation_reports/kc/4kc1 | HTTPS FTP |
-Related structure data
Related structure data | 4kc2C 4kc4C 3ioiS C: citing same article (ref.) S: Starting model for refinement |
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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: 33735.012 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-MN / |
#3: Chemical | ChemComp-BHE / |
#4: Chemical | ChemComp-WS1 / |
#5: Water | ChemComp-HOH / |
Sequence details | GLY266 AND ALA268 ARE THE CORRECT IDENTITIES AT THIS POSITION. THESE TWO MUTATIONS MAKE THE PROTEIN ...GLY266 AND ALA268 ARE THE CORRECT IDENTITIES |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 13% or 15% PEG 3350, 50 mM or 150 mM ammonium sulfate and 50 mM MOPS pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. all: 51220 / Num. obs: 51220 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.397 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.47 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3IOI Resolution: 1.5→42.3 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1686 / WRfactor Rwork: 0.1342 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9069 / SU B: 2.472 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0774 / SU Rfree: 0.0672 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.067 / Stereochemistry target values: Refmac 5 dictionary Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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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 max: 210.53 Å2 / Biso mean: 16.3456 Å2 / Biso min: 6.26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→42.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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