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- PDB-4xzi: Crystal structure of human Aldose Reductase complexed with NADP+ ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xzi | ||||||
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Title | Crystal structure of human Aldose Reductase complexed with NADP+ and JF0049 | ||||||
![]() | Aldose reductase | ||||||
![]() | OXIDOREDUCTASE / TIM barrel / Aldose reductase / diabetes / Halogenated compound / Cytosolic | ||||||
Function / homology | ![]() 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 / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / L-ascorbic acid biosynthetic process / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / daunorubicin metabolic process / doxorubicin metabolic process / epithelial cell maturation / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / carbohydrate metabolic process / electron transfer activity / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cousido-Siah, A. / Ruiz, F.X. / Mitschler, A. / Dominguez, M. / de Lera, A.R. / Farres, J. / Pares, X. / Podjarny, A. | ||||||
![]() | ![]() Title: Structural Determinants of the Selectivity of 3-Benzyluracil-1-acetic Acids toward Human Enzymes Aldose Reductase and AKR1B10. Authors: Ruiz, F.X. / Cousido-Siah, A. / Porte, S. / Dominguez, M. / Crespo, I. / Rechlin, C. / Mitschler, A. / de Lera, A.R. / Martin, M.J. / de la Fuente, J.A. / Klebe, G. / Pares, X. / Farres, J. / Podjarny, A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.6 KB | Display | ![]() |
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PDB format | ![]() | 60.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 19.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xzhC ![]() 4xzlC ![]() 4xzmC ![]() 4xznC ![]() 1us0S 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 35898.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-F49 / [ |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10 mM Tris-HCl, pH 8.0, 20% polyethylene glycol, PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 12391 / % possible obs: 99.1 % / Redundancy: 4.2 % / Rsym value: 0.08 / Net I/σ(I): 15.25 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.06 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1US0 Resolution: 2.45→37.032 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.24 / 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 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→37.032 Å
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Refine LS restraints |
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LS refinement shell |
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