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Yorodumi- PDB-2pdi: Human aldose reductase mutant L300A complexed with zopolrestat at... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pdi | ||||||
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Title | Human aldose reductase mutant L300A complexed with zopolrestat at 1.55 A. | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / TIM 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 / 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: 1.55 Å | ||||||
Authors | Steuber, H. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Merging the binding sites of aldose and aldehyde reductase for detection of inhibitor selectivity-determining features. Authors: Steuber, H. / Heine, A. / Podjarny, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pdi.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pdi.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 2pdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/2pdi ftp://data.pdbj.org/pub/pdb/validation_reports/pd/2pdi | HTTPS FTP |
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-Related structure data
Related structure data | 2pd5C 2pd9C 2pdbC 2pdcC 2pdfC 2pdgC 2pdhC 2pdjC 2pdkC 2pdlC 2pdmC 2pdnC 2pdpC 2pdqC 2pduC 2pdwC 2pdxC 2pdyC 1el3S C: citing same article (ref.) 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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Details | The asymmetric unit contains one biological monomer. |
-Components
#1: Protein | Mass: 35856.262 Da / Num. of mol.: 1 / Mutation: L300A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALR2 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P15121, aldose reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-ZST / |
#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: 2.2 Å3/Da / Density % sol: 43.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20 % PEG 6000 in 120 mM ammonium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 10, 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: 1.55→50 Å / Num. all: 41753 / Num. obs: 41753 / % possible obs: 93.3 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.026 / Rsym value: 0.026 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.063 / Mean I/σ(I) obs: 13.2 / Num. unique all: 1036 / Rsym value: 0.063 / % possible all: 46.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1el3 Resolution: 1.55→30 Å / Num. parameters: 11792 / Num. restraintsaints: 10715 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND 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: 1 / Occupancy sum hydrogen: 2520 / Occupancy sum non hydrogen: 2940 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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