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Yorodumi- PDB-1t40: Crystal structure of human aldose reductase complexed with NADP a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t40 | ||||||
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Title | Crystal structure of human aldose reductase complexed with NADP and IDD552 at ph 5 | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / aldose reductase / ternary complex / inhibitor binding | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ruiz, F. / Hazemann, I. / Mitschler, A. / Chevrier, B. / Schneider, T. / Joachimiak, A. / Karplus, M. / Podjarny, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: The crystallographic structure of the aldose reductase-IDD552 complex shows direct proton donation from tyrosine 48. Authors: Ruiz, F. / Hazemann, I. / Mitschler, A. / Joachimiak, A. / Schneider, T. / Karplus, M. / Podjarny, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t40.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t40.ent.gz | 62.2 KB | Display | PDB format |
PDBx/mmJSON format | 1t40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/1t40 ftp://data.pdbj.org/pub/pdb/validation_reports/t4/1t40 | HTTPS FTP |
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-Related 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-ID5 / [ |
#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: 1.7 Å3/Da / Density % sol: 24 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 6000, AMMONIUM CITRATE, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Nov 1, 2000 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→18 Å / Num. all: 29192 / Num. obs: 29192 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.4 / % possible all: 80 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→7.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1066073.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.3842 Å2 / ksol: 0.452308 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.8 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→7.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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