[English] 日本語
Yorodumi- PDB-5en4: Complex of 17-beta-hydroxysteroid dehydrogenase type 14 with inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5en4 | ||||||
---|---|---|---|---|---|---|---|
Title | Complex of 17-beta-hydroxysteroid dehydrogenase type 14 with inhibitor. | ||||||
Components | 17-beta-hydroxysteroid dehydrogenase 14 | ||||||
Keywords | OXIDOREDUCTASE / inhibitor complex / steroid dehydrogenase | ||||||
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: 1.52 Å | ||||||
Authors | Bertoletti, N. / Braun, F. / Marchais-Oberwinkler, S. / Heine, A. / Klebe, G. | ||||||
Funding support | Germany, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5en4.cif.gz | 152.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5en4.ent.gz | 121.9 KB | Display | PDB format |
PDBx/mmJSON format | 5en4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5en4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5en4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5en4_validation.xml.gz | 12 KB | Display | |
Data in CIF | 5en4_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/5en4 ftp://data.pdbj.org/pub/pdb/validation_reports/en/5en4 | HTTPS FTP |
-Related structure data
Related structure data | 5l7tC 5l7wC 5l7yC 1ydeS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 28343.420 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 |
---|---|
#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-5Q6 / [ |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.9 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 6000 20% Hepes 0.1M DMSO 5% / PH range: 7-8 |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→46.8 Å / Num. obs: 44532 / % possible obs: 99.9 % / Redundancy: 14.6 % / Rsym value: 0.053 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.52→1.61 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 6.6 / % possible all: 99.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YDE Resolution: 1.52→46.772 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 9.94 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→46.772 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|