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- PDB-5liw: Crystal structure of human AKR1B10 complexed with NADP+ and the i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5liw | ||||||
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Title | Crystal structure of human AKR1B10 complexed with NADP+ and the inhibitor MK319 | ||||||
![]() | Aldo-keto reductase family 1 member B10 | ||||||
![]() | OXIDOREDUCTASE / alpha-beta TIM barrel / cytosol / aldo-keto reductase / halogenated ligand | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Cousido-Siah, A. / Ruiz, F.X. / Mitschler, A. / Fanfrlik, J. / Kamlar, M. / Vesely, J. / Hobza, P. / Podjarny, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.4 KB | Display | ![]() |
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PDB format | ![]() | 63.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5likC ![]() 5liuC ![]() 5lixC ![]() 5liyC ![]() 1zuaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() 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 | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.02 % |
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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: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 3, 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: 1.75→50 Å / Num. obs: 33155 / % possible obs: 92.4 % / Redundancy: 2.6 % / Rsym value: 0.05 / Net I/σ(I): 19.03 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3.32 / % possible all: 81.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ZUA Resolution: 1.75→23.088 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 20.76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→23.088 Å
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Refine LS restraints |
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LS refinement shell |
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