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Yorodumi- PDB-4qr6: Human Aldose Reductase complexed with a ligand with an IDD struct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qr6 | ||||||
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Title | Human Aldose Reductase complexed with a ligand with an IDD structure (2-[2-(1,3-benzothiazol-2-ylmethylcarbamoyl)-5-fluoro-phenoxy]acetic acid) at 1.05 A | ||||||
Components | Aldose reductase | ||||||
Keywords | oxidoreductase/oxidoreductase inhibitor / TIM BARREL / oxidoreductase-oxidoreductase inhibitor complex | ||||||
Function / homology | Function and homology information glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / 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 / retinal dehydrogenase activity / epithelial cell maturation / 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: 1.05 Å | ||||||
Authors | Rechlin, C. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To be Published Title: Aldose Reductase: How expensive is the opening of the specificity pocket? IDD ligands under investigation Authors: Rechlin, C. / Scheer, F. / Toth, P. / Heine, A. / Diederich, W. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qr6.cif.gz | 156.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qr6.ent.gz | 122 KB | Display | PDB format |
PDBx/mmJSON format | 4qr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qr6_validation.pdf.gz | 950.1 KB | Display | wwPDB validaton report |
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Full document | 4qr6_full_validation.pdf.gz | 949.9 KB | Display | |
Data in XML | 4qr6_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 4qr6_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/4qr6 ftp://data.pdbj.org/pub/pdb/validation_reports/qr/4qr6 | HTTPS FTP |
-Related structure data
Related structure data | 4puwC 4q7bC 4qbxC 2duxS C: citing same article (ref.) 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 (E. coli) / Strain (production host): BL21 gold / References: UniProt: P15121, aldose reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-37V / { |
#4: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE CONTAINS ILE RESIDUES AT THAT POSITION |
-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: 43.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Crystallization solution: 50 mM di-Ammoniumhydrogen citrate pH 5.0 PEG6000= 5 % (m/V) DTT= 5.15 g/L NADP+= 0.66 g/L and Human Aldose Reductase= 15 mg/ml.Afterwards the crystals were soaked ...Details: Crystallization solution: 50 mM di-Ammoniumhydrogen citrate pH 5.0 PEG6000= 5 % (m/V) DTT= 5.15 g/L NADP+= 0.66 g/L and Human Aldose Reductase= 15 mg/ml.Afterwards the crystals were soaked into Tris 100 mM 25% (m/V) PEG6000 pH 8.0 saturated with the inhibitor.The well solution was for crystallization was 120mM di-Ammonium hydrogen citrate with 20% PEG6000 pH 5.0., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 10, 2014 / Details: Silicon, active surface 50 nm Rh-coated |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→50 Å / Num. all: 142734 / Num. obs: 142734 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 7.978 Å2 / Rsym value: 0.043 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 1.05→1.07 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 7043 / Rsym value: 0.466 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DUX Resolution: 1.05→16.916 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 12.73 / 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: 1.05→16.916 Å
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Refine LS restraints |
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LS refinement shell |
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