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Yorodumi- PDB-3c3u: Crystal structure of AKR1C1 in complex with NADP and 3,5-dichloro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c3u | ||||||
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Title | Crystal structure of AKR1C1 in complex with NADP and 3,5-dichlorosalicylic acid | ||||||
Components | Aldo-keto reductase family 1 member C1 | ||||||
Keywords | OXIDOREDUCTASE / Aldo-keto reductase / 20 alpha hydroxysteroid dehydrogenase / AKR1C1 / Cytoplasm / NADP | ||||||
Function / homology | Function and homology information 3beta-hydroxy-5beta-steroid dehydrogenase activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / androsterone dehydrogenase (B-specific) activity / indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 3(or 17)beta-hydroxysteroid dehydrogenase ...3beta-hydroxy-5beta-steroid dehydrogenase activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / androsterone dehydrogenase (B-specific) activity / indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 3(or 17)beta-hydroxysteroid dehydrogenase / indanol dehydrogenase activity / testosterone dehydrogenase [NAD(P)] activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / response to organophosphorus / phenanthrene 9,10-monooxygenase activity / cellular response to jasmonic acid stimulus / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / dihydrotestosterone 17-beta-dehydrogenase activity / androsterone dehydrogenase activity / intestinal cholesterol absorption / 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 / carboxylic acid binding / estradiol 17-beta-dehydrogenase [NAD(P)] activity / aldo-keto reductase (NADPH) activity / bile acid metabolic process / bile acid and bile salt transport / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / daunorubicin metabolic process / doxorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / bile acid binding / aldose reductase (NADPH) activity / Prednisone ADME / retinoid metabolic process / prostaglandin metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Retinoid metabolism and transport / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / digestion / epithelial cell differentiation / xenobiotic metabolic process / cholesterol homeostasis / positive regulation of reactive oxygen species metabolic process / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Dhagat, U. / El-Kabbani, O. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Selectivity determinants of inhibitor binding to human 20alpha-hydroxysteroid dehydrogenase: crystal structure of the enzyme in ternary complex with coenzyme and the potent inhibitor 3,5-dichlorosalicylic acid Authors: Dhagat, U. / Endo, S. / Sumii, R. / Hara, A. / El-Kabbani, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c3u.cif.gz | 88.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c3u.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 3c3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/3c3u ftp://data.pdbj.org/pub/pdb/validation_reports/c3/3c3u | HTTPS FTP |
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-Related structure data
Related structure data | 1mrqS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 4 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 4 - 323 / Label seq-ID: 4 - 323
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-Components
#1: Protein | Mass: 36839.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C1, DDH, DDH1 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): pKKDD1 References: UniProt: Q04828, 20alpha-hydroxysteroid dehydrogenase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-NAP / |
#4: Chemical | ChemComp-C2U / |
#5: 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: 2.21 Å3/Da / Density % sol: 44.42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, 25% Polyglycol monomethylether 550, 0.01M Zinc sulphate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 13, 2007 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 27340 / Num. obs: 26329 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 2.99 % / Rmerge(I) obs: 0.0504 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.2299 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2076 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MRQ Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.876 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.143 / ESU R Free: 0.134 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.654 Å2
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Refine analyze | Luzzati coordinate error obs: 0.195 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2592 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0 Å
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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