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Yorodumi- PDB-5l7y: 17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l7y | |||||||||
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Title | 17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex with a non-steroidal inhibitor. | |||||||||
Components | 17-beta-hydroxysteroid dehydrogenase 14 | |||||||||
Keywords | OXIDOREDUCTASE / hydroxysteroid dehydrogenase / inhibitor 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: 1.912 Å | |||||||||
Authors | Bertoletti, N. / Braun, F. / Marchais-Oberwinkler, S. / Heine, A. / Klebe, G. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: J. Med. Chem. / Year: 2016 Title: First Structure-Activity Relationship of 17 beta-Hydroxysteroid Dehydrogenase Type 14 Nonsteroidal Inhibitors and Crystal Structures in Complex with the Enzyme. Authors: Braun, F. / Bertoletti, N. / Moller, G. / Adamski, J. / Steinmetzer, T. / Salah, M. / Abdelsamie, A.S. / van Koppen, C.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 | 5l7y.cif.gz | 109.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l7y.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 5l7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l7y_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5l7y_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5l7y_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 5l7y_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/5l7y ftp://data.pdbj.org/pub/pdb/validation_reports/l7/5l7y | HTTPS FTP |
-Related structure data
Related structure data | 5en4SC 5l7tC 5l7wC 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(DE3) (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-NA / | ||
#4: Chemical | #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: 2.43 Å3/Da / Density % sol: 49.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: CHES 0.1 M pH 9.50 tri-sodium-citrate 1.00 M DMSO 5% PH range: 8-9.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.7999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7999 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. obs: 21943 / % possible obs: 98.9 % / Redundancy: 7.17 % / Rsym value: 0.088 / Net I/σ(I): 16.75 |
Reflection shell | Resolution: 1.91→2.03 Å / Redundancy: 6.66 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.71 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EN4 Resolution: 1.912→46.31 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.912→46.31 Å
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Refine LS restraints |
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LS refinement shell |
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