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Yorodumi- PDB-6ipb: Crystal Structure of the Cofactor-binding Domain of the Human Pha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ipb | ||||||
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Title | Crystal Structure of the Cofactor-binding Domain of the Human Phase II Drug Metabolism Enzyme UGT2B15 | ||||||
Components | UDP-glucuronosyltransferase 2B15 | ||||||
Keywords | TRANSFERASE / Drug metabolism / UGT / Glycosyltransferase / Tartaric acid | ||||||
Function / homology | Function and homology information glucuronosyltransferase / cellular glucuronidation / Glucuronidation / glucuronosyltransferase activity / Paracetamol ADME / estrogen metabolic process / Aspirin ADME / steroid metabolic process / xenobiotic metabolic process / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å | ||||||
Authors | Zhang, L. / Xie, W. / Wang, C. | ||||||
Citation | Journal: Biochem. Pharmacol. / Year: 2019 Title: Insight into tartrate inhibition patterns in vitro and in vivo based on cocrystal structure with UDP-glucuronosyltransferase 2B15. Authors: Zhang, L. / Zhu, L. / Qu, W. / Wu, F. / Hu, M. / Xie, W. / Liu, Z. / Wang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ipb.cif.gz | 157.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ipb.ent.gz | 123.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ipb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/6ipb ftp://data.pdbj.org/pub/pdb/validation_reports/ip/6ipb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 21342.635 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UGT2B15, UGT2B8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P54855, glucuronosyltransferase #2: Chemical | ChemComp-TLA / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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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: 42.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 18% PEG 3350, 0.2M Na-Tartrate, 0.2M KCl, 2% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.775→70.91 Å / Num. obs: 64886 / % possible obs: 99.25 % / Redundancy: 6.6 % / CC1/2: 0.991 / Rpim(I) all: 0.04 / Rrim(I) all: 0.104 / Net I/σ(I): 22.64 |
Reflection shell | Resolution: 1.78→1.84 Å / Mean I/σ(I) obs: 2.737 / Num. unique obs: 6779 / CC1/2: 0.902 / Rpim(I) all: 0.206 / Rrim(I) all: 0.521 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.78→70.91 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.425 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.098 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.014 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→70.91 Å
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Refine LS restraints |
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