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Yorodumi- PDB-5m2f: Crystal structure of human AKR1B10 complexed with NADP+ and the s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m2f | ||||||
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Title | Crystal structure of human AKR1B10 complexed with NADP+ and the synthetic retinoid UVI2008 | ||||||
Components | Aldo-keto reductase family 1 member B10 | ||||||
Keywords | OXIDOREDUCTASE / TIM barrel / Aldo-Keto Reductase / Synthetic Retinoid / Cytosolic | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.503 Å | ||||||
Authors | Ruiz, F.X. / Cousido-Siah, A. / Mitschler, A. / Porte, S. / Alvarez, S. / Dominguez, M. / Alvarez, R. / de Lera, A.R. / Pares, X. / Farres, J. / Podjarny, A. | ||||||
Citation | Journal: Chem. Biol. Interact. / Year: 2017 Title: Structural basis for the inhibition of AKR1B10 by the C3 brominated TTNPB derivative UVI2008. Authors: Ruiz, F.X. / Crespo, I. / Alvarez, S. / Porte, S. / Gimenez-Dejoz, J. / Cousido-Siah, A. / Mitschler, A. / de Lera, A.R. / Pares, X. / Podjarny, A. / Farres, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m2f.cif.gz | 86 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m2f.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 5m2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m2f_validation.pdf.gz | 1005.9 KB | Display | wwPDB validaton report |
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Full document | 5m2f_full_validation.pdf.gz | 1011.6 KB | Display | |
Data in XML | 5m2f_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 5m2f_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/5m2f ftp://data.pdbj.org/pub/pdb/validation_reports/m2/5m2f | HTTPS FTP |
-Related structure data
Related structure data | 1zuaS 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: 36447.121 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-UV8 / |
#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: 2.49 Å3/Da / Density % sol: 50.65 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.729 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 16, 2013 |
Radiation | Monochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.729 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 55875 / % possible obs: 99.66 % / Redundancy: 2.6 % / Rsym value: 0.055 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.3 / % possible all: 98.22 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZUA Resolution: 1.503→40.359 Å / Cross valid method: FREE R-VALUE / σ(F): 2.69 / Phase error: 24.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.503→40.359 Å
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Refine LS restraints |
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LS refinement shell |
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