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Yorodumi- PDB-1x98: Crystal structure of Aldose Reductase complexed with 2S4R (Stereo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x98 | ||||||
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Title | Crystal structure of Aldose Reductase complexed with 2S4R (Stereoisomer of Fidarestat, 2S4S) | ||||||
Components | Aldose Reductase | ||||||
Keywords | OXIDOREDUCTASE / Eight strandard alpha/beta barrel / active site / the C-terminal end of the barrel | ||||||
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 / retinal dehydrogenase activity / epithelial cell maturation / 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: 1.3 Å | ||||||
Authors | El-Kabbani, O. / Darmanin, C. / Oka, M. / Schulze-Briese, C. / Tomizaki, T. / Hazemann, I. / Mitschler, A. / Podjarny, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2004 Title: High-Resolution Structures of Human Aldose Reductase Holoenzyme in Complex with Stereoisomers of the Potent Inhibitor Fidarestat: Stereospecific Interaction between the Enzyme and a Cyclic Imide Type Inhibitor Authors: El-Kabbani, O. / Darmanin, C. / Oka, M. / Schulze-Briese, C. / Tomizaki, T. / Hazemann, I. / Mitschler, A. / Podjarny, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x98.cif.gz | 96.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x98.ent.gz | 70.6 KB | Display | PDB format |
PDBx/mmJSON format | 1x98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x98_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1x98_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1x98_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 1x98_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/1x98 ftp://data.pdbj.org/pub/pdb/validation_reports/x9/1x98 | HTTPS FTP |
-Related structure data
Related structure data | 1x96C 1x97C 1pwmS S: Starting model for refinement C: citing same article (ref.) |
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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) / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P15121, aldose reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-CIT / |
#4: Chemical | ChemComp-FIS / ( |
#5: 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: 1.82 Å3/Da / Density % sol: 34.6 % |
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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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.79999 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 3, 2002 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.79999 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 91523 / Num. obs: 88919 / % possible obs: 97.15 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.054 / Mean I/σ(I) obs: 24.3 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PWM Resolution: 1.3→10 Å / Num. parameters: 13211 / Num. restraintsaints: 11952 / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Luzzati coordinate error obs: 0.075 Å / Num. disordered residues: 139 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3042.12 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→10 Å
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Refine LS restraints |
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