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Yorodumi- PDB-3frj: Crystal Structure of 11b-Hydroxysteroid Dehydrogenase-1 (11b-HSD1... -
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-Basic information
Entry | Database: PDB / ID: 3frj | ||||||
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Title | Crystal Structure of 11b-Hydroxysteroid Dehydrogenase-1 (11b-HSD1) in Complex with Piperidyl Benzamide Inhibitor | ||||||
Components | Corticosteroid 11-beta-Dehydrogenase, Isozyme 1 | ||||||
Keywords | OXIDOREDUCTASE / Endoplasmic reticulum / Glycoprotein / Lipid metabolism / Membrane / NADP / Polymorphism / Signal-anchor / Steroid metabolism / Transmembrane | ||||||
Function / homology | Function and homology information 11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development ...11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development / NADP binding / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein homodimerization activity / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Wang, Z. / Sudom, A. / Walker, N.P. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Discovery and optimization of piperidyl benzamide derivatives as a novel class of 11beta-HSD1 inhibitors. Authors: Rew, Y. / McMinn, D.L. / Wang, Z. / He, X. / Hungate, R.W. / Jaen, J.C. / Sudom, A. / Sun, D. / Tu, H. / Ursu, S. / Villemure, E. / Walker, N.P. / Yan, X. / Ye, Q. / Powers, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3frj.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3frj.ent.gz | 93.8 KB | Display | PDB format |
PDBx/mmJSON format | 3frj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/3frj ftp://data.pdbj.org/pub/pdb/validation_reports/fr/3frj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31836.875 Da / Num. of mol.: 2 / Mutation: C272S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11B1, HSD11, HSD11L / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): DH10a References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase #2: Chemical | #3: Chemical | ChemComp-A49 / | #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: 3.68 Å3/Da / Density % sol: 66.59 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 6.4 Details: 36% P400, 0.1 M Hepes 7.5, pH 6.4, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2005 / Details: 3X3 CCD ARRAY |
Radiation | Monochromator: DOUBLE-CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→75.378 Å / Num. all: 38729 / Num. obs: 38706 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.5 % / Rmerge(I) obs: 0.056 / Rsym value: 0.059 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 5.7 / Rsym value: 0.458 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.3→75.34 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.404 / SU ML: 0.133 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.635 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→75.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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