+Open data
-Basic information
Entry | Database: PDB / ID: 2f2k | ||||||
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Title | Aldose reductase tertiary complex with NADPH and DEG | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / INHIBITOR / GLUTATHIONE / TERTIARY COMPLEX / DICARBOXYETHYL GLUTATHIONE | ||||||
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 / L-ascorbic acid biosynthetic process / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / epithelial cell maturation / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / electron transfer activity / carbohydrate metabolic process / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Singh, R. / White, M.A. / Ramana, K.V. / Petrash, J.M. / Watowich, S.J. / Bhatnagar, A. / Srivastava, S.K. | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Structure of a glutathione conjugate bound to the active site of aldose reductase. Authors: Singh, R. / White, M.A. / Ramana, K.V. / Petrash, J.M. / Watowich, S.J. / Bhatnagar, A. / Srivastava, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f2k.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f2k.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 2f2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/2f2k ftp://data.pdbj.org/pub/pdb/validation_reports/f2/2f2k | HTTPS FTP |
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-Related structure data
Related structure data | 1adsS S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Plasmid: PMON5997 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P15121, aldose reductase |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-TGG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: SODIUM CITRATE, PHOSPHATE, PEG 4000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jun 17, 2003 / Details: MULTILAYER |
Radiation | Monochromator: GOEBEL MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→30 Å / Num. all: 22676 / Num. obs: 22676 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.94→1.99 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.307 / % possible all: 96 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ADS Resolution: 1.94→29.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1147192.3 / Data cutoff low absF: 0 / Isotropic thermal model: VARIABLE / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: VARIABLE B-FACTOR RESTRAINTS: SIGMA= (B**2/ * WGT), WGT=10
Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.3553 Å2 / ksol: 0.365062 e/Å3 | Displacement parameters | Biso mean: 21.4 Å2 |
Refine analyze |
Refinement step | Cycle: LAST / Resolution: 1.94→29.88 Å |
Refine LS restraints |
LS refinement shell | Resolution: 1.94→1.97 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 20 |
Xplor file |
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