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- PDB-3p2v: Novel Benzothiazepine Inhibitor in Complex with human Aldose Reductase -
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Open data
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Basic information
Entry | Database: PDB / ID: 3p2v | ||||||
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Title | Novel Benzothiazepine Inhibitor in Complex with human Aldose Reductase | ||||||
![]() | Aldose reductase | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / TIM barrel / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
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 | ![]() ![]() | ||||||
![]() | Koch, C. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Ligand-induced fit affects binding modes and provokes changes in crystal packing of aldose reductase Authors: Koch, C. / Heine, 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 | ![]() | 87.5 KB | Display | ![]() |
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PDB format | ![]() | 63.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lenC ![]() 3m0iC ![]() 3m64C ![]() 3mb9C ![]() 3mc5C ![]() 2fz8S 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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Components
#1: Protein | Mass: 35898.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-NAP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE CONFLICT HAS BEEN DESCRIBED IN J BIOL CHEM 1989 SEP 5; 264(25): 14775-7 BY CHUNG S, ...THIS SEQUENCE CONFLICT HAS BEEN DESCRIBED IN J BIOL CHEM 1989 SEP 5; 264(25): 14775-7 BY CHUNG S, ET AL., PUBMED ID 2504709 | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 44.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20% PEG 6000, 120mM citrate buffer, 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: Apr 22, 2006 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→50 Å / Num. all: 29903 / Num. obs: 29903 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rsym value: 0.042 / Net I/σ(I): 20.67 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.237 / % possible all: 45.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FZ8 Resolution: 1.69→20 Å / Num. parameters: 11718 / Num. restraintsaints: 11243 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & 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: 14 / Occupancy sum hydrogen: 2518 / Occupancy sum non hydrogen: 2836.84 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→20 Å
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Refine LS restraints |
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