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- PDB-6zt2: 17beta-hydroxysteroid dehydrogenase type 14 variant S205 in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zt2 | ||||||
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Title | 17beta-hydroxysteroid dehydrogenase type 14 variant S205 in complex with 3-chloro-2,6-difluorophenol | ||||||
![]() | 17-beta-hydroxysteroid dehydrogenase 14 | ||||||
![]() | OXIDOREDUCTASE / Inhibitor Complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Badran, M.J. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: 17beta-hydroxysteroid dehydrogenase type 14 variant S205 in complex with 3-chloro-2,6-difluorophenol Authors: Badran, M.J. / Heine, A. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.8 KB | Display | ![]() |
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PDB format | ![]() | 46 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 815.7 KB | Display | ![]() |
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Full document | ![]() | 815.9 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5icmS S: Starting model for refinement |
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Similar structure data |
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Links
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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
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/BGC.gif)
![](data/chem/img/BGC.gif)
#1: Protein | Mass: 28329.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: wild type - S205 variant / Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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#2: Sugar | ChemComp-BGC / |
-Non-polymers , 4 types, 98 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/QPK.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/QPK.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NAD / |
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#4: Chemical | ChemComp-QPK / |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: HEPES 0.1M pH 7 PEG6000 25% w/v DMSO 2.5% 2-hydroxypropyl-beta-cyclodextrin 5mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 20921 / % possible obs: 99.7 % / Redundancy: 8.5 % / Biso Wilson estimate: 24.09 Å2 / CC1/2: 0.99 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.95→2.06 Å / Num. unique obs: 3271 / CC1/2: 0.89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ICM Resolution: 1.95→46.37 Å / SU ML: 0.1846 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.2184 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→46.37 Å
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Refine LS restraints |
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LS refinement shell |
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