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Yorodumi- PDB-4puw: Human Aldose Reductase complexed with a ligand with an IDD struct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4puw | ||||||
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Title | Human Aldose Reductase complexed with a ligand with an IDD structure (2-[5-fluoro-2-(prop-2-ynylcarbamoyl)phenoxy]acetic acid) at 1.12 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 / 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: 1.12 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. / Heine, A. / Scheer, F. / Toth, P. / 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 | 4puw.cif.gz | 162 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4puw.ent.gz | 125.8 KB | Display | PDB format |
PDBx/mmJSON format | 4puw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/4puw ftp://data.pdbj.org/pub/pdb/validation_reports/pu/4puw | HTTPS FTP |
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-Related structure data
Related structure data | 4q7bC 4qbxC 4qr6C 2duxS 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 / 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-2WQ / [ |
#3: Chemical | ChemComp-CIT / |
#4: Chemical | ChemComp-NAP / |
#5: Water | ChemComp-HOH / |
Sequence details | AUTHORS HAVE INDICATED THAT THE SEQUENCING RESULT OF THE PLASMID USED SHOWED A ILE IN POSITION 4. ...AUTHORS HAVE INDICATED THAT THE SEQUENCING |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 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. 9 microliter of the crystallization ...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. 9 microliter of the crystallization solution were mixed with 3 microliter of a 5 mM solution of the inhibitor in 120 mM di-Ammoniumhydrogen citrate pH 5.0 with 25 % (m/V) PEG 6000 and 5 % DMSO, 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: Jul 18, 2013 / 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: 1.12→50 Å / Num. all: 117148 / Num. obs: 117148 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 7.351 Å2 / Rsym value: 0.059 / Net I/σ(I): 15.99 |
Reflection shell | Resolution: 1.12→1.14 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.44 / Num. unique all: 5781 / Rsym value: 0.426 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2dux Resolution: 1.12→18.486 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 12.74 / Stereochemistry target values: Engh & Huber
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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: 1.12→18.486 Å
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Refine LS restraints |
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LS refinement shell |
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