[English] 日本語
![](img/lk-miru.gif)
- PDB-2nvc: Human Aldose Reductase complexed with novel naphtho[1,2-d]isothia... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2nvc | ||||||
---|---|---|---|---|---|---|---|
Title | Human Aldose Reductase complexed with novel naphtho[1,2-d]isothiazole acetic acid derivative (3) | ||||||
![]() | Aldose reductase | ||||||
![]() | OXIDOREDUCTASE / TIM barrel / protein-ligand complex / aldose reductase | ||||||
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: Evidence for a novel binding site conformer of aldose reductase in ligand-bound state Authors: Steuber, H. / Zentgraf, M. / La Motta, C. / Sartini, S. / Heine, A. / Klebe, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 86.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 62.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1002.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1010 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nvdC ![]() 1el3S C: citing same article ( S: Starting model for refinement |
---|---|
Similar 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.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-ITA / { |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.4 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 120mM ammonium citrate, 20% PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 15, 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: 1.65→50 Å / Num. all: 32788 / Num. obs: 32788 / % possible obs: 89.3 % / Redundancy: 2 % / Rmerge(I) obs: 0.03 / Rsym value: 0.03 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 3.1 / Num. unique all: 887 / Rsym value: 0.247 / % possible all: 48.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EL3 Resolution: 1.65→19.55 Å / Num. parameters: 11502 / Num. restraintsaints: 10867 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 7 / Occupancy sum hydrogen: 2526 / Occupancy sum non hydrogen: 2840 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→19.55 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|