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- PDB-8tic: 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: 8tic | ||||||
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Title | Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with compound 1 | ||||||
![]() | N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 | ||||||
![]() | TRANSFERASE / acetylglucosaminyltransferase / inhibitor | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Sudom, A. / Min, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Imidazolone as an Amide Bioisostere in the Development of beta-1,3- N -Acetylglucosaminyltransferase 2 (B3GNT2) Inhibitors. Authors: Jackson, J.J. / Siegmund, A.C. / Bai, W.J. / Reed, A.B. / Birkholz, A.B. / Campuzano, I.D.G. / Crequer-Grandhomme, A. / Hu, R. / Modak, R.V. / Sudom, A. / Javier, N. / Sanders, C. / Lo, M.C. ...Authors: Jackson, J.J. / Siegmund, A.C. / Bai, W.J. / Reed, A.B. / Birkholz, A.B. / Campuzano, I.D.G. / Crequer-Grandhomme, A. / Hu, R. / Modak, R.V. / Sudom, A. / Javier, N. / Sanders, C. / Lo, M.C. / Xie, F. / Cee, V.J. / Manzanillo, P. / Allen, J.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 286.2 KB | Display | ![]() |
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PDB format | ![]() | 230.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8sz3C ![]() 8tjcC ![]() 7jhkS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 |
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 46085.898 Da / Num. of mol.: 4 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 , 2 types, 6 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 #3: Sugar | |
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-Non-polymers , 4 types, 69 molecules ![](data/chem/img/FKX.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-FKX / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 0.17 M sodium acetate, 0.08 M Tris pH 8.5, 25.5% PEG 4000, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→29.98 Å / Num. obs: 46965 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 44.13 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.392 / Rpim(I) all: 0.132 / Rrim(I) all: 0.415 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.7→2.79 Å / Redundancy: 10 % / Rmerge(I) obs: 2.503 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4559 / CC1/2: 0.328 / Rpim(I) all: 0.822 / Rrim(I) all: 2.639 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7JHK Resolution: 2.7→29.98 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29.98 Å
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Refine LS restraints |
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LS refinement shell |
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