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Yorodumi- PDB-5liy: Crystal structure of human AKR1B10 complexed with NADP+ and the i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5liy | ||||||
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Title | Crystal structure of human AKR1B10 complexed with NADP+ and the inhibitor MK204 | ||||||
Components | Aldo-keto reductase family 1 member B10 | ||||||
Keywords | OXIDOREDUCTASE / alpha-beta TIM barrel / cytosol / aldo-keto reductase / halogenated ligand | ||||||
Function / homology | Function and homology information indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / aldo-keto reductase (NADPH) activity / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / all-trans-retinol dehydrogenase (NADP+) activity ...indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / aldo-keto reductase (NADPH) activity / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / all-trans-retinol dehydrogenase (NADP+) activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / Retinoid metabolism and transport / lysosome / mitochondrion / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Cousido-Siah, A. / Ruiz, F.X. / Mitschler, A. / Fanfrlik, J. / Kamlar, M. / Vesely, J. / Hobza, P. / Podjarny, A. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: IDD388 Polyhalogenated Derivatives as Probes for an Improved Structure-Based Selectivity of AKR1B10 Inhibitors. Authors: Cousido-Siah, A. / Ruiz, F.X. / Fanfrlik, J. / Gimenez-Dejoz, J. / Mitschler, A. / Kamlar, M. / Vesely, J. / Ajani, H. / Pares, X. / Farres, J. / Hobza, P. / Podjarny, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5liy.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5liy.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 5liy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/5liy ftp://data.pdbj.org/pub/pdb/validation_reports/li/5liy | HTTPS FTP |
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-Related structure data
Related structure data | 5likC 5liuC 5liwC 5lixC 1zuaS 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: 36300.887 Da / Num. of mol.: 1 / Mutation: K125R, V301L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B10, AKR1B11 / Production host: Escherichia coli (E. coli) References: UniProt: O60218, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-DQP / { |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 30% PEG 6000, 100 mM sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 21542 / % possible obs: 90.6 % / Redundancy: 2.3 % / Rsym value: 0.079 / Net I/σ(I): 9.95 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.92 / % possible all: 83.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZUA Resolution: 2.05→28.237 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 2.25 / Phase error: 23.57 / 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: 2.05→28.237 Å
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Refine LS restraints |
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LS refinement shell |
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