[English] 日本語
Yorodumi- PDB-1pwl: Crystal structure of human Aldose Reductase complexed with NADP a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pwl | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human Aldose Reductase complexed with NADP and Minalrestat | ||||||
Components | aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / ALDOSE REDUCTASE / ATOMIC RESOLUTION / TERNARY COMPLEX / INHIBITOR BINDING | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | El-Kabbani, O. / Darmanin, C. / Schneider, T.R. / Hazemann, I. / Ruiz, F. / Oka, M. / Joachimiak, A. / Schulze-Briese, C. / Tomizaki, T. / Mitschler, A. / Podjarny, A. | ||||||
Citation | Journal: PROTEINS / Year: 2004 Title: Ultrahigh resolution drug design. II. Atomic resolution structures of human aldose reductase holoenzyme complexed with Fidarestat and Minalrestat: implications for the binding of cyclic imide inhibitors Authors: El-Kabbani, O. / Darmanin, C. / Schneider, T.R. / Hazemann, I. / Ruiz, F. / Oka, M. / Joachimiak, A. / Schulze-Briese, C. / Tomizaki, T. / Mitschler, A. / Podjarny, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pwl.cif.gz | 169.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pwl.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 1pwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/1pwl ftp://data.pdbj.org/pub/pdb/validation_reports/pw/1pwl | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P15121, aldose reductase |
---|---|
#2: Chemical | ChemComp-BFI / |
#3: Chemical | ChemComp-NAP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.64 Å3/Da / Density % sol: 24.9 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 6000, ammonium citrate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9 / Wavelength: 0.9 Å | |||||||||
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 30, 2001 | |||||||||
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.1→50 Å / Num. all: 115145 / Num. obs: 115145 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.63 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 25.6 | |||||||||
Reflection shell | Resolution: 1.1→1.61 Å / Redundancy: 3.13 % / Rmerge(I) obs: 0.0921 / Mean I/σ(I) obs: 11.75 / % possible all: 81.5 | |||||||||
Reflection | *PLUS % possible obs: 92.6 % / Rmerge(I) obs: 0.041 | |||||||||
Reflection shell | *PLUS % possible obs: 81.5 % |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ALDOSE REDUCTASE HOLOENZYME Resolution: 1.1→10 Å / Num. parameters: 28902 / Num. restraintsaints: 36371 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.4 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.035 Å / Num. disordered residues: 95 / Occupancy sum hydrogen: 2390.21 / Occupancy sum non hydrogen: 2967.93 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.1 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.124 / Rfactor Rwork: 0.099 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|