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Yorodumi- PDB-8b3r: Human Aldose Reductase Mutant A299G/L300G in Complex with a Ligan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b3r | ||||||
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Title | Human Aldose Reductase Mutant A299G/L300G in Complex with a Ligand with an IDD Structure ({5-fluoro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid) | ||||||
Components | Aldo-keto reductase family 1 member B1 | ||||||
Keywords | OXIDOREDUCTASE / human Aldose Reductase / hAR / Aldo-keto-reductase / A299G/L300G mutant / IDD_06 / nadp+ / diabetes / ligand in transient pocket / no flip | ||||||
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: 0.96 Å | ||||||
Authors | Hubert, L.-S. / Heine, A. / Klebe, G. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Human Aldose Reductase Mutant A299G/L300G in Complex with a Ligand with an IDD Structure ({5-fluoro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid) Authors: Hubert, L.-S. / Heine, A. / Klebe, G. / Scheer, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b3r.cif.gz | 282.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b3r.ent.gz | 191.3 KB | Display | PDB format |
PDBx/mmJSON format | 8b3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b3r_validation.pdf.gz | 962.9 KB | Display | wwPDB validaton report |
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Full document | 8b3r_full_validation.pdf.gz | 967 KB | Display | |
Data in XML | 8b3r_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 8b3r_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/8b3r ftp://data.pdbj.org/pub/pdb/validation_reports/b3/8b3r | HTTPS FTP |
-Related structure data
Related structure data | 4prrS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35828.207 Da / Num. of mol.: 1 / Mutation: A299G, L300G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1, ALR2 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P15121, NADP-retinol dehydrogenase, D/L-glyceraldehyde reductase, allyl-alcohol dehydrogenase, aldose reductase | ||||
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#2: Chemical | ChemComp-NAP / | ||||
#3: Chemical | ChemComp-30L / { | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-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: 44.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 50 mM Di-Ammoniumhydrogen citrate pH 5: 15 mg/mL hAR, 5.2 mg/mL DTT, 0.7 mg/mL NADP+, 10% (w/v) PEG 6000; Reservoir: 120 mM Di-Ammoniumhydrogen citrate pH 5, 20% (w/v) PEG 6000; Soaking: 120 ...Details: 50 mM Di-Ammoniumhydrogen citrate pH 5: 15 mg/mL hAR, 5.2 mg/mL DTT, 0.7 mg/mL NADP+, 10% (w/v) PEG 6000; Reservoir: 120 mM Di-Ammoniumhydrogen citrate pH 5, 20% (w/v) PEG 6000; Soaking: 120 mM di-ammonium hydrogen citrate pH 5.0, 25% PEG 6000, saturated with ligand |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 0.96→47.3 Å / Num. obs: 173283 / % possible obs: 92.8 % / Redundancy: 6 % / Biso Wilson estimate: 6.97 Å2 / CC1/2: 1 / Rsym value: 0.04 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 0.96→1.02 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 5.2 / Num. unique obs: 24641 / CC1/2: 0.94 / Rsym value: 0.3 / % possible all: 81.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PRR Resolution: 0.96→39.66 Å / SU ML: 0.0533 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 9.8915 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.96→39.66 Å
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Refine LS restraints |
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LS refinement shell |
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