+Open data
-Basic information
Entry | Database: PDB / ID: 4yvp | ||||||
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Title | Crystal Structure of AKR1C1 complexed with glibenclamide | ||||||
Components | Aldo-keto reductase family 1 member C1 | ||||||
Keywords | Oxidoreductase/Oxidoreductase inhibitor / AKR1C1 inhibitor / Oxidoreductase-Oxidoreductase inhibitor complex | ||||||
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 / androsterone dehydrogenase (B-specific) activity / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 3(or 17)alpha-hydroxysteroid dehydrogenase / 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 / androsterone dehydrogenase (B-specific) activity / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 3(or 17)alpha-hydroxysteroid dehydrogenase / 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 / : / cellular response to jasmonic acid stimulus / dihydrotestosterone 17-beta-dehydrogenase activity / androsterone dehydrogenase activity / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / intestinal cholesterol absorption / response to organophosphorus / 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 / carboxylic acid binding / 17beta-estradiol 17-dehydrogenase / 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 / retinoid metabolic process / Prednisone ADME / digestion / prostaglandin metabolic process / epithelial cell differentiation / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Retinoid metabolism and transport / 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: 2.6 Å | ||||||
Authors | Zhao, Y. / Zheng, X. / Zhang, H. / Hu, X. | ||||||
Citation | Journal: Chem.Biol.Interact. / Year: 2015 Title: In vitro inhibition of AKR1Cs by sulphonylureas and the structural basis Authors: Zhao, Y. / Zheng, X. / Zhang, H. / Zhai, J. / Zhang, L. / Li, C. / Zeng, K. / Chen, Y. / Li, Q. / Hu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yvp.cif.gz | 144.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yvp.ent.gz | 112.8 KB | Display | PDB format |
PDBx/mmJSON format | 4yvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yvp_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4yvp_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4yvp_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 4yvp_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/4yvp ftp://data.pdbj.org/pub/pdb/validation_reports/yv/4yvp | HTTPS FTP |
-Related structure data
Related structure data | 4yvvC 4yvxC 4zfcC 3ntyS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36839.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Condon plus) References: UniProt: Q04828, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, 20alpha-hydroxysteroid dehydrogenase, indanol dehydrogenase, trans-1,2- ...References: UniProt: Q04828, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, 20alpha-hydroxysteroid dehydrogenase, indanol dehydrogenase, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.58 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 23-27% (w/v) PEG 4000, 100 mM Hepes, 10mM CaCl2, 0.4M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Aug 27, 2014 / Details: OXFORD ONYX CCD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→88.385 Å / Num. all: 20327 / Num. obs: 19305 / % possible obs: 99.81 % / Redundancy: 3.9 % / Rpim(I) all: 0.14 / Rrim(I) all: 0.277 / Net I/σ(I): 5.1 / Num. measured all: 79376 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NTY Resolution: 2.6→88.38 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.834 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 19.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→88.38 Å
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Refine LS restraints |
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