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- PDB-5m2f: Crystal structure of human AKR1B10 complexed with NADP+ and the s... -
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Open data
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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 | ||||||
![]() | Aldo-keto reductase family 1 member B10 | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.4 KB | Display | ![]() |
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PDB format | ![]() | 64.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 797.9 KB | Display | ![]() |
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Full document | ![]() | 805.6 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zuaS S: Starting model for refinement |
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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: 36447.121 Da / Num. of mol.: 1 / Mutation: K125R, V301L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: O60218, ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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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