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- PDB-4wdx: 17beta-HSD5 in complex with [4-(2-hydroxyethyl)piperidin-1-yl](5-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wdx | ||||||
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Title | 17beta-HSD5 in complex with [4-(2-hydroxyethyl)piperidin-1-yl](5-methyl-1H-indol-2-yl)methanone | ||||||
![]() | Aldo-keto reductase family 1 member C3 | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / aldo-keto reductase inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Amano, Y. / Yamaguchi, T. | ||||||
![]() | ![]() Title: Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding. Authors: Amano, Y. / Yamaguchi, T. / Niimi, T. / Sakashita, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.3 KB | Display | ![]() |
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PDB format | ![]() | 109.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4wdtC ![]() 4wduC ![]() 4wdwC ![]() 4xvdC ![]() 4xveC ![]() 4wds ![]() 4wdv C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37967.355 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P42330, ![]() #2: Chemical | ![]() #3: Chemical | #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.71 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M HEPES, 0.2M ammonium dihydrogen phosphate, 20-25% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jul 16, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.64→59.51 Å / Num. obs: 76592 / % possible obs: 95.7 % / Redundancy: 3.6 % / Net I/σ(I): 6.7 |
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Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.64→14.27 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.346 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 27.64 Å2
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Refinement step | Cycle: 1 / Resolution: 1.64→14.27 Å
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Refine LS restraints |
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