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Yorodumi- PDB-2f38: Crystal structure of prostaglandin F synathase containing bimatoprost -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f38 | ||||||
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Title | Crystal structure of prostaglandin F synathase containing bimatoprost | ||||||
Components | Aldo-keto reductase family 1 member C3 | ||||||
Keywords | OXIDOREDUCTASE / Prostaglandin F synthase / AKR1C3 / PGF2alpha fromation / PGH2 / bimatoprost / catalytic mechanism | ||||||
Function / homology | Function and homology information prostaglandin-F synthase / testosterone 17beta-dehydrogenase (NADP+) / prostaglandin D2 11-ketoreductase activity / ketoreductase activity / prostaglandin F synthase activity / cellular response to prostaglandin stimulus / cellular response to corticosteroid stimulus / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / negative regulation of retinoic acid biosynthetic process ...prostaglandin-F synthase / testosterone 17beta-dehydrogenase (NADP+) / prostaglandin D2 11-ketoreductase activity / ketoreductase activity / prostaglandin F synthase activity / cellular response to prostaglandin stimulus / cellular response to corticosteroid stimulus / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / negative regulation of retinoic acid biosynthetic process / macromolecule metabolic process / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / Delta4-3-oxosteroid 5beta-reductase activity / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / farnesol catabolic process / geranylgeranyl reductase activity / 3alpha-hydroxysteroid 3-dehydrogenase / : / cellular response to jasmonic acid stimulus / regulation of testosterone biosynthetic process / dihydrotestosterone 17-beta-dehydrogenase activity / androsterone dehydrogenase activity / testosterone biosynthetic process / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / RA biosynthesis pathway / regulation of retinoic acid receptor signaling pathway / cellular response to prostaglandin D stimulus / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / retinal metabolic process / testosterone 17-beta-dehydrogenase (NADP+) activity / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / aldo-keto reductase (NADPH) activity / all-trans-retinol dehydrogenase (NAD+) activity / cyclooxygenase pathway / positive regulation of endothelial cell apoptotic process / prostaglandin H2 endoperoxidase reductase activity / all-trans-retinol dehydrogenase (NADP+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / daunorubicin metabolic process / doxorubicin metabolic process / bile acid binding / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / prostaglandin metabolic process / renal absorption / steroid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Retinoid metabolism and transport / keratinocyte differentiation / cellular response to calcium ion / cellular response to starvation / response to nutrient / male gonad development / positive regulation of reactive oxygen species metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / extracellular exosome / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Komoto, J. / Yamada, T. / Watanabe, K. / Woodward, D.F. / Takusagawa, F. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Prostaglandin F2alpha formation from prostaglandin H2 by prostaglandin F synthase (PGFS): crystal structure of PGFS containing bimatoprost. Authors: Komoto, J. / Yamada, T. / Watanabe, K. / Woodward, D.F. / Takusagawa, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f38.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f38.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 2f38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f38_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2f38_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2f38_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 2f38_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/2f38 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/2f38 | HTTPS FTP |
-Related structure data
Related structure data | 1ry0S S: Starting model for refinement |
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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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Details | Monomeric protein containing one NADPH and one bimatoprost. |
-Components
#1: Protein | Mass: 36896.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C3, DDH1, KIAA0119, PGFS / Plasmid: pUC-hLuFS / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 References: UniProt: P42330, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase, EC: 1.1.1.213, prostaglandin-F synthase, 17beta-estradiol 17-dehydrogenase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-15M / ( |
#4: 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: 2.26 Å3/Da / Density % sol: 45.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.0 mM BMP, 1.0 mM NADPH, 0.14 M NaCl, 50 mM MES, 26% PEG-8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 5, 2005 / Details: confocal optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 19525 / Num. obs: 19525 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2→2.1 Å / % possible all: 63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1RY0 Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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