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Yorodumi- PDB-8tjc: Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tjc | ||||||
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Title | Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with compound 8a | ||||||
Components | N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 | ||||||
Keywords | TRANSFERASE / acetylglucosaminyltransferase / inhibitor | ||||||
Function / homology | Function and homology information 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 / keratan sulfate biosynthetic process / poly-N-acetyllactosamine biosynthetic process / Keratan sulfate biosynthesis / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation / cellular response to leukemia inhibitory factor ...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 / keratan sulfate biosynthetic process / poly-N-acetyllactosamine 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Sudom, A. / Min, X. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tjc.cif.gz | 291.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tjc.ent.gz | 235.7 KB | Display | PDB format |
PDBx/mmJSON format | 8tjc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/8tjc ftp://data.pdbj.org/pub/pdb/validation_reports/tj/8tjc | HTTPS FTP |
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-Related structure data
Related structure data | 8sz3C 8ticC 7jhkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: B3GNT2, B3GALT7, B3GNT1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9NY97, N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase |
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-Sugars , 6 types, 7 molecules
#2: Polysaccharide | 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 | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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 |
#4: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 |
#5: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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 |
#6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 |
#9: Sugar |
-Non-polymers , 4 types, 134 molecules
#7: Chemical | ChemComp-MN / #8: Chemical | ChemComp-HI8 / ( #10: Chemical | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 0.1 M Tris 8.8, 0.16 M Sodium acetate, 25% PEG4000, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2019 |
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→47.01 Å / Num. obs: 88402 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 50.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.046 / Rrim(I) all: 0.168 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.2→2.4 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4513 / CC1/2: 0.398 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JHK Resolution: 2.2→47.01 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.8 / 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: 2.2→47.01 Å
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Refine LS restraints |
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LS refinement shell |
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