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Yorodumi- PDB-3ghu: Human aldose reductase in complex with NADP+ and the inhibitor ID... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ghu | ||||||
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Title | Human aldose reductase in complex with NADP+ and the inhibitor IDD594. Investigation of global effects of radiation damage on protein structure. Forth stage of radiation damage. | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / Acetylation / Cataract / Cytoplasm / NADP / Phosphoprotein / Polymorphism | ||||||
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 / epithelial cell maturation / retinal dehydrogenase activity / 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: 1.2 Å | ||||||
Authors | Petrova, T. / Ginell, S. / Hazemann, I. / Mitschler, A. / Podjarny, A. / Joachimiak, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: X-ray-radiation-induced cooperative atomic movements in protein. Authors: Petrova, T. / Lunin, V.Y. / Ginell, S. / Hazemann, I. / Lazarski, K. / Mitschler, A. / Podjarny, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ghu.cif.gz | 197.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ghu.ent.gz | 157.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ghu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ghu_validation.pdf.gz | 1017.7 KB | Display | wwPDB validaton report |
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Full document | 3ghu_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3ghu_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 3ghu_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/3ghu ftp://data.pdbj.org/pub/pdb/validation_reports/gh/3ghu | HTTPS FTP |
-Related structure data
Related structure data | 3ghrC 3ghsC 3ghtC 1us0S 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) / Gene: AKR1B1, ALDR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P15121, aldose reductase |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-LDT / |
#4: Chemical | ChemComp-CIT / |
#5: Water | ChemComp-HOH / |
Sequence details | AUTHORS STATE THAT RESIDUE NUMBER 4 IS ILE. ELECTRON DENSITY FOR THIS RESIDUE IS VERY CLEAR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.65 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: The co-crystallization with IDD594 was carried out at room temperature (ratios protein/coenzyme/inhibitor = 1/2/2), pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91996 Å |
Detector | Type: ADSC QUANTUM Q315r / Detector: CCD / Date: Aug 20, 2007 Details: 1.02-M FLAT MIRROR MADE OF ZERODUR PROVIDING VERTICAL FOCUSING AND REJECTION OF HARMONIC CONTAMINATION |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR UTILIZING A SI-111 AND SAGITAL HORIZONTAL FOCUSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91996 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. all: 92143 / Num. obs: 92143 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.023 / Rsym value: 0.033 / Net I/σ(I): 33.8 |
Reflection shell | Resolution: 1.2→1.23 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 3 / Num. unique all: 5869 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1US0 Resolution: 1.2→50 Å / σ(F): 4 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.2→50 Å
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