+Open data
-Basic information
Entry | Database: PDB / ID: 1ef3 | ||||||
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Title | FIDARESTAT BOUND TO HUMAN ALDOSE REDUCTASE | ||||||
Components | ALDOSE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / BETA BARREL / PROTEIN-INHIBITOR COMPLEX | ||||||
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: 2.8 Å | ||||||
Authors | Oka, M. / Matsumoto, Y. / Sugiyama, S. / Tsuruta, N. / Matsushima, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2000 Title: A potent aldose reductase inhibitor, (2S,4S)-6-fluoro-2', 5'-dioxospiro[chroman-4,4'-imidazolidine]-2-carboxamide (Fidarestat): its absolute configuration and interactions with the aldose ...Title: A potent aldose reductase inhibitor, (2S,4S)-6-fluoro-2', 5'-dioxospiro[chroman-4,4'-imidazolidine]-2-carboxamide (Fidarestat): its absolute configuration and interactions with the aldose reductase by X-ray crystallography. Authors: Oka, M. / Matsumoto, Y. / Sugiyama, S. / Tsuruta, N. / Matsushima, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ef3.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ef3.ent.gz | 93.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ef3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/1ef3 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/1ef3 | HTTPS FTP |
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-Related structure data
Related structure data | 1adsS 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: 35767.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: MUSCLESkeletal muscle / Production host: unidentified baculovirus / References: UniProt: P15121, aldose reductase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.77 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.8M ammonium sulfate, 2% PEG400, 0.1 M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 281 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Jul 6, 1998 / Details: A BENDED DOUBLE MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→999 Å / Num. obs: 15960 / % possible obs: 92.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.0705 |
Reflection shell | Resolution: 2.8→2.85 Å / % possible all: 81.7 |
Reflection | *PLUS Num. measured all: 27091 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ADS Resolution: 2.8→8 Å / σ(F): 2 / σ(I): 2
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Displacement parameters | Biso mean: 4.96 Å2 | ||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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