+Open data
-Basic information
Entry | Database: PDB / ID: 1eko | ||||||
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Title | PIG ALDOSE REDUCTASE COMPLEXED WITH IDD384 INHIBITOR | ||||||
Components | ALDOSE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / ALDOSE REDUCTASE / INHIBITION / DIABETES | ||||||
Function / homology | Function and homology information glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / prostaglandin H2 endoperoxidase reductase activity / all-trans-retinol dehydrogenase (NADP+) activity / retinal dehydrogenase activity / aldose reductase (NADPH) activity ...glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / prostaglandin H2 endoperoxidase reductase activity / all-trans-retinol dehydrogenase (NADP+) activity / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Podjarny, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: The structure of human aldose reductase bound to the inhibitor IDD384. Authors: Calderone, V. / Chevrier, B. / Van Zandt, M. / Lamour, V. / Howard, E. / Poterszman, A. / Barth, P. / Mitschler, A. / Lu, J. / Dvornik, D.M. / Klebe, G. / Kraemer, O. / Moorman, A.R. / Moras, D. / Podjarny, A. #1: Journal: J.AM.SOC.MASS.SPECTROM. / Year: 1999 Title: Binding of Aldose Reductase Inhibitors: Correlation of Crystallographic and Mass Spectrometric Studies Authors: Rogniaux, H. / Van Dorsselaer, A. / Barth, P. / Biellmann, J.F. / Barbanton, J. / van Zandt, M. / Chevrier, B. / Howard, E. / Mitschler, A. / Potier, N. / Urzhumtseva, L. / Moras, D. / Podjarny, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eko.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eko.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 1eko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/1eko ftp://data.pdbj.org/pub/pdb/validation_reports/ek/1eko | 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: 35824.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: EYE / Tissue: LENS / References: UniProt: P80276, aldose reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-I84 / [ |
#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: 2.56 Å3/Da / Density % sol: 51.87 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 6 MG/ML AR, 2.5% PEG 6000, 25 MM MESPH 6.2 (DROP), 20% PEG 6000, 25 MM MESPH 6.2 (RESERVOIR) , VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Rogniaux, H., (1999) J. Am. Soc. Mass Spectrom., 10, 635. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.91 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 8, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. all: 20372 / Num. obs: 19184 / % possible obs: 98.1 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.245 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ALDOSE REDUCTASE NATIVE Resolution: 2.2→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 18314069.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.8234 Å2 / ksol: 0.382389 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.4 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 9.8 % / Rfactor obs: 0.179 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 42.4 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.394 / % reflection Rfree: 11 % / Rfactor Rwork: 0.355 |