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Open data
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Basic information
Entry | Database: PDB / ID: 2pd9 | ||||||
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Title | Human aldose reductase mutant V47I complexed with fidarestat. | ||||||
![]() | Aldose reductase | ||||||
![]() | OXIDOREDUCTASE / protein-ligand complex / TIM-barrel | ||||||
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 | ![]() ![]() | ||||||
![]() | Steuber, H. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Merging the binding sites of aldose and aldehyde reductase for detection of inhibitor selectivity-determining features. Authors: Steuber, H. / Heine, A. / Podjarny, A. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.8 KB | Display | ![]() |
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PDB format | ![]() | 64.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2pd5C ![]() 2pdbC ![]() 2pdcC ![]() 2pdfC ![]() 2pdgC ![]() 2pdhC ![]() 2pdiC ![]() 2pdjC ![]() 2pdkC ![]() 2pdlC ![]() 2pdmC ![]() 2pdnC ![]() 2pdpC ![]() 2pdqC ![]() 2pduC ![]() 2pdwC ![]() 2pdxC ![]() 2pdyC ![]() 1el3S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The asymmetric unit contains one biological monomer. |
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Components
#1: Protein | Mass: 35912.367 Da / Num. of mol.: 1 / Mutation: V47I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-FID / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20 % PEG 6000 in 120 mM Ammonium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 14, 2006 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. all: 43127 / Num. obs: 43127 / % possible obs: 96.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 56.6 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.053 / Mean I/σ(I) obs: 24.4 / Num. unique all: 1337 / Rsym value: 0.053 / % possible all: 60.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1el3 Resolution: 1.55→30 Å / Num. parameters: 12092 / Num. restraintsaints: 10924 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 7 / Occupancy sum hydrogen: 2478 / Occupancy sum non hydrogen: 2989 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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