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- PDB-7jhn: Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7jhn | ||||||
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Title | Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with UDP and trisaccharide GlcNAc-beta1-3Gal-beta1-4GlcNAc | ||||||
![]() | N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 | ||||||
![]() | TRANSFERASE / glycosyltransferase / poly-N-acetyl-lactosamine | ||||||
Function / homology | ![]() N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase / : / UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity / poly-N-acetyllactosamine biosynthetic process / keratan sulfate biosynthetic process / Keratan sulfate biosynthesis / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation ...N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase / : / UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity / N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity / poly-N-acetyllactosamine biosynthetic process / keratan sulfate biosynthetic process / Keratan sulfate biosynthesis / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation / cellular response to leukemia inhibitory factor / axon guidance / sensory perception of smell / Golgi membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Hao, Y. / Huang, X. | ||||||
![]() | ![]() Title: Structures and mechanism of human glycosyltransferase beta 1,3-N-acetylglucosaminyltransferase 2 (B3GNT2), an important player in immune homeostasis. Authors: Hao, Y. / Crequer-Grandhomme, A. / Javier, N. / Singh, A. / Chen, H. / Manzanillo, P. / Lo, M.C. / Huang, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.5 KB | Display | ![]() |
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PDB format | ![]() | 66.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jhiSC ![]() 7jhkC ![]() 7jhlC ![]() 7jhmC ![]() 7jhoC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43300.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NY97, N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase |
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-Sugars , 3 types, 3 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#4: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 111 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MG / | ||
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#6: Chemical | ChemComp-UDP / | ||
#7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 24% PEG1500, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 87 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. obs: 17836 / % possible obs: 86.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.25 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.03 / Rrim(I) all: 0.058 / Χ2: 0.923 / Net I/σ(I): 11.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7JHI Resolution: 2.2→39.8938 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.56 / 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 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.41 Å2 / Biso mean: 38.9464 Å2 / Biso min: 4.85 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→39.8938 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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