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Yorodumi- PDB-4kc2: Structure of the blood group glycosyltransferase AAglyB in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kc2 | ||||||
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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 soluble form | ||||||
Keywords | Transferase/Transferase Inhibitor / GTA superfamily / blood group proteins / glycosyltransferase / Fuc-Gal / UDP-Gal / UDP-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: 1.7 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 | 4kc2.cif.gz | 142.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kc2.ent.gz | 108.1 KB | Display | PDB format |
PDBx/mmJSON format | 4kc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/4kc2 ftp://data.pdbj.org/pub/pdb/validation_reports/kc/4kc2 | HTTPS FTP |
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-Related structure data
Related structure data | 4kc1C 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
#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-WS2 / |
#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: 47.67 % |
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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: 1.7→50 Å / Num. all: 35437 / Num. obs: 35437 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.846 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 11.44 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.7→42.32 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.1892 / WRfactor Rwork: 0.1625 / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.8875 / SU B: 3.71 / SU ML: 0.065 / SU R Cruickshank DPI: 0.107 / SU Rfree: 0.1015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.102 / Stereochemistry target values: Refmac 5 dictionary / Details: U VALUES WITH TLS ADDED
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.85 Å2 / Biso mean: 13.989 Å2 / Biso min: 5.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→42.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 10.231 Å / Origin y: 20.288 Å / Origin z: -6.154 Å
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