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Yorodumi- PDB-8sz3: Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sz3 | ||||||
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Title | Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with compound 7j | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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 | 8sz3.cif.gz | 185.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sz3.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 8sz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sz3_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 8sz3_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 8sz3_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 8sz3_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/8sz3 ftp://data.pdbj.org/pub/pdb/validation_reports/sz/8sz3 | HTTPS FTP |
-Related structure data
Related structure data | 8ticC 8tjcC 7jhkS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 46085.898 Da / Num. of mol.: 2 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 #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | 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: 2.13 Å3/Da / Density % sol: 42.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 0.1 M Hepes pH 7.0, 0.2 M Sodium Acetate, 17% PEG 4000, 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: Mar 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→29.14 Å / Num. obs: 33310 / % possible obs: 98.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.041 / Rrim(I) all: 0.076 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.32→2.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3035 / Rpim(I) all: 0.309 / Rrim(I) all: 0.557 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JHK Resolution: 2.32→29.14 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.2015 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→29.14 Å
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Refine LS restraints |
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LS refinement shell |
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