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Yorodumi- PDB-3rx4: Crystal Structure of Human Aldose Reductase complexed with Sulind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rx4 | ||||||
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Title | Crystal Structure of Human Aldose Reductase complexed with Sulindac Sulfide | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / Aldose Reductase | ||||||
Function / homology | Function and homology information glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / L-ascorbic acid biosynthetic process / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / epithelial cell maturation / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / electron transfer activity / carbohydrate metabolic process / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zheng, X. / Chen, J. / Luo, H. / Hu, X. | ||||||
Citation | Journal: Febs Lett. / Year: 2012 Title: The molecular basis for inhibition of sulindac and its metabolites towards human aldose reductase. Authors: Zheng, X. / Zhang, L. / Zhai, J. / Chen, Y. / Luo, H. / Hu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rx4.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rx4.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 3rx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/3rx4 ftp://data.pdbj.org/pub/pdb/validation_reports/rx/3rx4 | HTTPS FTP |
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-Related structure data
Related structure data | 3rx2C 3rx3C 3s3gC 1us0S 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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Unit cell |
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-Components
#1: Protein | Mass: 38069.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P15121, aldose reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-SFI / |
#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: 2.07 Å3/Da / Density % sol: 40.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 50mM ammonium citrate, pH5.0, 7.5% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-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: Apr 17, 2011 |
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→24.776 Å / Num. all: 21142 / Num. obs: 21142 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2→2.11 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1US0 Resolution: 2→24.776 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 18.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.455 Å2 / ksol: 0.334 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→24.776 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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