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Yorodumi- PDB-5hs6: Human 17beta-hydroxysteroid dehydrogenase type 14 in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hs6 | |||||||||
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Title | Human 17beta-hydroxysteroid dehydrogenase type 14 in complex with Estrone | |||||||||
Components | 17-beta-hydroxysteroid dehydrogenase 14 | |||||||||
Keywords | OXIDOREDUCTASE / 17bHSD14 / Estrone complex | |||||||||
Function / homology | Function and homology information Estrogen biosynthesis / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)] activity / steroid catabolic process / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | |||||||||
Authors | Bertoletti, N. / Marchais-Oberwinkler, S. / Heine, A. / Klebe, G. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: J.Med.Chem. / Year: 2016 Title: New Insights into Human 17 beta-Hydroxysteroid Dehydrogenase Type 14: First Crystal Structures in Complex with a Steroidal Ligand and with a Potent Nonsteroidal Inhibitor. Authors: Bertoletti, N. / Braun, F. / Lepage, M. / Moller, G. / Adamski, J. / Heine, A. / Klebe, G. / Marchais-Oberwinkler, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hs6.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hs6.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 5hs6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/5hs6 ftp://data.pdbj.org/pub/pdb/validation_reports/hs/5hs6 | HTTPS FTP |
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-Related structure data
Related structure data | 5icmC 5icsC 5js6C 5jsfC 5en4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28682.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): pLysS References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-J3Z / ( |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: CHES 0.1M, tri-sodium citrate 1M / PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. obs: 18613 / % possible obs: 99.7 % / Redundancy: 7.52 % / Rsym value: 0.083 / Net I/σ(I): 15.86 |
Reflection shell | Resolution: 2.02→2.14 Å / Redundancy: 7.57 % / Mean I/σ(I) obs: 4.3 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EN4 Resolution: 2.02→46.106 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→46.106 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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