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- PDB-3bcj: Crystal structure of Aldose Reductase complexed with 2S4R (Stereo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bcj | ||||||
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Title | Crystal structure of Aldose Reductase complexed with 2S4R (Stereoisomer of Fidarestat, 2S4S) at 0.78 A | ||||||
![]() | Aldose reductase | ||||||
![]() | OXIDOREDUCTASE / Aldo-Keto Reductases / Diabetes / Drug Design / Polyl Pathway / Acetylation / Cataract / Cytoplasm / NADP / Polymorphism | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Zhao, H.T. / El-Kabbani, O. | ||||||
![]() | ![]() Title: Unusual Binding Mode of the 2S4R Stereoisomer of the Potent Aldose Reductase Cyclic Imide Inhibitor Fidarestat (2S4S) in the 15 K Crystal Structure of the Ternary Complex Refined at 0.78 A ...Title: Unusual Binding Mode of the 2S4R Stereoisomer of the Potent Aldose Reductase Cyclic Imide Inhibitor Fidarestat (2S4S) in the 15 K Crystal Structure of the Ternary Complex Refined at 0.78 A Resolution: Implications for the Inhibition Mechanism Authors: Zhao, H.T. / Hazemann, I. / Mitschler, A. / Carbone, V. / Joachimiak, A. / Ginell, S. / Podjarny, A. / El-Kabbani, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.1 KB | Display | ![]() |
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PDB format | ![]() | 148.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pwn 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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Unit cell |
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Components
#1: Protein | Mass: 35898.340 Da / Num. of mol.: 1 / Fragment: Human Aldose Reductase Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-CIT / |
#4: Chemical | ChemComp-FIS / ( |
#5: Water | ChemComp-HOH / |
Sequence details | FOR THIS CONFLICT, REFER TO REFERENCE 2 IN THE DATABASE, ALDR_HUMAN, P15121 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.01 % |
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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 |
-Data collection
Diffraction | Mean temperature: 15 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Mar 1, 2005 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 0.78→99 Å / Num. all: 345646 / Num. obs: 336314 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 2.12 % |
Reflection shell | Resolution: 0.78→0.81 Å / Redundancy: 2 % / Num. unique all: 325713 / % possible all: 93.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PWN ![]() 1pwn Resolution: 0.78→10 Å / Num. parameters: 32941 / Num. restraintsaints: 8836 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The close contacts are due to either double conformation of amino acid side chains or partial occupancies by water molecules observed at very high resolution.
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Refine analyze | Luzzati coordinate error obs: 0.031 Å / Num. disordered residues: 109 / Occupancy sum hydrogen: 2435.26 / Occupancy sum non hydrogen: 3204.13 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.78→10 Å
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Refine LS restraints |
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