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Yorodumi- PDB-4xzi: Crystal structure of human Aldose Reductase complexed with NADP+ ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xzi | ||||||
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Title | Crystal structure of human Aldose Reductase complexed with NADP+ and JF0049 | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / TIM barrel / Aldose reductase / diabetes / Halogenated compound / Cytosolic | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Cousido-Siah, A. / Ruiz, F.X. / Mitschler, A. / Dominguez, M. / de Lera, A.R. / Farres, J. / Pares, X. / Podjarny, A. | ||||||
Citation | Journal: Chemmedchem / Year: 2015 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xzi.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xzi.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 4xzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/4xzi ftp://data.pdbj.org/pub/pdb/validation_reports/xz/4xzi | HTTPS FTP |
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-Related structure data
Related structure data | 4xzhC 4xzlC 4xzmC 4xznC 1us0S S: Starting model for refinement C: citing same article (ref.) |
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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 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.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15121, aldose reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-F49 / [ |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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