+Open data
-Basic information
Entry | Database: PDB / ID: 4qxi | ||||||
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Title | Crystal structure of human AR complexed with NADP+ and AK198 | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / TIM barrel / Aldose reductase / diabetes / Halogenated compound / Cytosolic | ||||||
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: 0.867 Å | ||||||
Authors | Cousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Fanfrlik, J. / Hobza, P. / Podjarny, A.D. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2015 Title: The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition. Authors: Fanfrlik, J. / Ruiz, F.X. / Kadlcikova, A. / Rezac, J. / Cousido-Siah, A. / Mitschler, A. / Haldar, S. / Lepsik, M. / Kolar, M.H. / Majer, P. / Podjarny, A.D. / Hobza, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qxi.cif.gz | 167.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qxi.ent.gz | 130.6 KB | Display | PDB format |
PDBx/mmJSON format | 4qxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/4qxi ftp://data.pdbj.org/pub/pdb/validation_reports/qx/4qxi | HTTPS FTP |
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-Related structure data
Related structure data | 1us0S 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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-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 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15121, aldose reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-I98 / { |
#4: Water | ChemComp-HOH / |
Sequence details | THIS RESIDUE IS BASED ON GENBANK DATABASE AAA51714. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 50 mM ammonium citrate, 20% PEG 6000, 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: SLS / Beamline: X06DA / Wavelength: 0.8 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 3, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 0.867→50 Å / Num. all: 219664 / Num. obs: 219664 / % possible obs: 87.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 6.31 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1US0 Resolution: 0.867→27.589 Å / SU ML: 0.06 / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Phase error: 12.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.867→27.589 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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