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- PDB-1fdu: HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221L CO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fdu | ||||||
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Title | HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221L COMPLEXED WITH ESTRADIOL AND NADP+ | ||||||
![]() | 17-BETA-HYDROXYSTEROID DEHYDROGENASE | ||||||
![]() | DEHYDROGENASE / 17-BETA-HYDROXYSTEROID / MUTANT / ESTRADIOL / NADP | ||||||
Function / homology | ![]() estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity ...estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid biosynthetic process / estrogen metabolic process / NADP+ binding / lysosome organization / The canonical retinoid cycle in rods (twilight vision) / small molecule binding / catalytic activity / adipose tissue development / skeletal muscle tissue development / steroid binding / bone development / NADP binding / gene expression / protein homodimerization activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mazza, C. / Breton, R. / Housset, D. / Fontecilla-Camps, J.-C. | ||||||
![]() | ![]() Title: Unusual charge stabilization of NADP+ in 17beta-hydroxysteroid dehydrogenase. Authors: Mazza, C. / Breton, R. / Housset, D. / Fontecilla-Camps, J.C. #1: ![]() Title: Human Type I 17Beta-Hydroxysteroid Dehydrogenase: Site Directed Mutagenesis and X-Ray Crystallography Structure-Function Analysis Authors: Mazza, C. #2: ![]() Title: The Structure of a Complex of Human 17Beta-Hydroxysteroid Dehydrogenase with Estradiol and Nadp+ Identifies Two Principal Targets for the Design of Inhibitors Authors: Breton, R. / Housset, D. / Mazza, C. / Fontecilla-Camps, J.C. #3: ![]() Title: Structure of Human Estrogenic 17 Beta-Hydroxysteroid Dehydrogenase at 2.20 A Resolution Authors: Ghosh, D. / Pletnev, V.Z. / Zhu, D.W. / Wawrzak, Z. / Duax, W.L. / Pangborn, W. / Labrie, F. / Lin, S.X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 234.3 KB | Display | ![]() |
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PDB format | ![]() | 189.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 54.5 KB | Display | |
Data in CIF | ![]() | 71.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1fdvC ![]() 1fdwC ![]() 1fdtS S: Starting model for refinement 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 34948.961 Da / Num. of mol.: 4 / Mutation: H221L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EST / #4: Chemical | ChemComp-NAP / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.96 Å3/Da / Density % sol: 69 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.3 Details: PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, 100 MM SODIUM PHOSPHATE BUFFER PH 6.3, 1 MM NADP+, 100 MM NACL; THEN SOAKED IN 30 % PEG 4000, 100 MM HEPES PH 6.5, 100 MM NACL, 0.5 MM ESTRADIOL, 1 MM NADP+ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ![]() ![]() |
Radiation | Monochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9827 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. obs: 57170 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 3.96 % / Rsym value: 0.092 |
Reflection shell | Resolution: 2.7→2.83 Å / Redundancy: 2.36 % / Rsym value: 0.277 / % possible all: 32 |
Reflection | *PLUS Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS % possible obs: 32 % / Rmerge(I) obs: 0.277 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FDT Resolution: 2.7→10 Å / σ(F): 2
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Displacement parameters | Biso mean: 25.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |