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Yorodumi- PDB-5y7n: Crystal structure of AKR1B10 in complex with NADP+ and Androst-4-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y7n | ||||||
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Title | Crystal structure of AKR1B10 in complex with NADP+ and Androst-4-ene-3-beta-6-alpha-diol | ||||||
Components | Aldo-keto reductase family 1 member B10 | ||||||
Keywords | OXIDOREDUCTASE / AKR1B10 / steroid / complex / inhibitor / ANTITUMOR PROTEIN | ||||||
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: 2.5 Å | ||||||
Authors | Hong, Z. / Liping, Z. / Cuiyun, L. / Wei, Z. | ||||||
Citation | Journal: To Be Published Title: Structural determinants for the inhibition of AKR1B10 by steroids Authors: Hong, Z. / Cuiyun, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y7n.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y7n.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 5y7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y7n_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5y7n_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5y7n_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 5y7n_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/5y7n ftp://data.pdbj.org/pub/pdb/validation_reports/y7/5y7n | HTTPS FTP |
-Related structure data
Related structure data | 4jihS 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: 36071.543 Da / Num. of mol.: 1 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-8QL / ( |
#4: 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: 2.53 Å3/Da / Density % sol: 51.39 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 100mM Tris, 30-35% PEG 6000, 3-5% 1,6-Hexanediol, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: May 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25.94 Å / Num. obs: 12535 / % possible obs: 99.87 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.518 / Num. unique obs: 1828 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JIH Resolution: 2.5→25.94 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.106 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.711 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.637 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→25.94 Å
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