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- PDB-6x5r: Human Alpha-1,6-fucosyltransferase (FUT8) bound to GDP and A2-Asn -
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Open data
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Basic information
Entry | Database: PDB / ID: 6x5r | ||||||
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Title | Human Alpha-1,6-fucosyltransferase (FUT8) bound to GDP and A2-Asn | ||||||
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![]() | TRANSFERASE / Glycosyl transferase / Fucosyl transferase / GT-B fold / Inverting | ||||||
Function / homology | ![]() glycoprotein 6-alpha-L-fucosyltransferase / glycoprotein 6-alpha-L-fucosyltransferase activity / receptor metabolic process / GDP-L-fucose metabolic process / alpha-(1->6)-fucosyltransferase activity / N-glycan fucosylation / Reactions specific to the complex N-glycan synthesis pathway / L-fucose catabolic process / oligosaccharide biosynthetic process / regulation of cellular response to oxidative stress ...glycoprotein 6-alpha-L-fucosyltransferase / glycoprotein 6-alpha-L-fucosyltransferase activity / receptor metabolic process / GDP-L-fucose metabolic process / alpha-(1->6)-fucosyltransferase activity / N-glycan fucosylation / Reactions specific to the complex N-glycan synthesis pathway / L-fucose catabolic process / oligosaccharide biosynthetic process / regulation of cellular response to oxidative stress / N-glycan processing / respiratory gaseous exchange by respiratory system / protein N-linked glycosylation via asparagine / fibroblast migration / protein N-linked glycosylation / Golgi cisterna membrane / transforming growth factor beta receptor signaling pathway / integrin-mediated signaling pathway / SH3 domain binding / regulation of gene expression / Maturation of spike protein / in utero embryonic development / viral protein processing / Golgi membrane / Golgi apparatus / extracellular exosome / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kadirvelraj, R. / Wood, Z.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Characterizing human alpha-1,6-fucosyltransferase (FUT8) substrate specificity and structural similarities with related fucosyltransferases. Authors: Boruah, B.M. / Kadirvelraj, R. / Liu, L. / Ramiah, A. / Li, C. / Zong, G. / Bosman, G.P. / Yang, J.Y. / Wang, L.X. / Boons, G.J. / Wood, Z.A. / Moremen, K.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 417.4 KB | Display | ![]() |
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PDB format | ![]() | 337.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 41.1 KB | Display | |
Data in CIF | ![]() | 60.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x5hC ![]() 6x5sC ![]() 6x5tC ![]() 6x5uC ![]() 2de0S C: citing same article ( 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
-Protein / Protein/peptide / Sugars , 3 types, 6 molecules ABCD
#1: Protein | Mass: 61845.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9BYC5, glycoprotein 6-alpha-L-fucosyltransferase #2: Protein/peptide | Mass: 332.376 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Polysaccharide | |
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-Non-polymers , 5 types, 621 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | A2-Asn was purified as a glycosylated peptide, and proteolyzed to small fragments containing the ...A2-Asn was purified as a glycosylated peptide, and proteolyzed to small fragments containing the glycosylated asparagine |
Source details | A2-Asn was purified from egg yolk powder |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.48 Å3/Da / Density % sol: 81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.0 M Lithium sulfate, 10 mM Nickel chloride, 100 mM Tris pH 8.5 Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 8, 2017 |
Radiation | Monochromator: Si (111) Rosenbaum-Rock double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→49.409 Å / Num. obs: 124545 / % possible obs: 99.3 % / Redundancy: 10.4 % / Biso Wilson estimate: 43 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.153 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8849 / CC1/2: 0.761 / Rrim(I) all: 1.5 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DE0 Resolution: 2.4→49.409 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→49.409 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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