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Yorodumi- PDB-4jii: Crystal Structure Of AKR1B10 Complexed With NADP+ And Zopolrestat -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jii | ||||||
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Title | Crystal Structure Of AKR1B10 Complexed With NADP+ And Zopolrestat | ||||||
Components | Aldo-keto reductase family 1 member B10 | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / TIM barrel / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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: 2.2 Å | ||||||
Authors | Zhang, L. / Zheng, X. / Zhang, H. / Zhao, Y. / Chen, K. / Zhai, J. / Hu, X. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Febs Lett. / Year: 2013 Title: Inhibitor selectivity between aldo-keto reductase superfamily members AKR1B10 and AKR1B1: Role of Trp112 (Trp111). Authors: Zhang, L. / Zhang, H. / Zhao, Y. / Li, Z. / Chen, S. / Zhai, J. / Chen, Y. / Xie, W. / Wang, Z. / Li, Q. / Zheng, X. / Hu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jii.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jii.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jii_validation.pdf.gz | 974 KB | Display | wwPDB validaton report |
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Full document | 4jii_full_validation.pdf.gz | 975.9 KB | Display | |
Data in XML | 4jii_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 4jii_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/4jii ftp://data.pdbj.org/pub/pdb/validation_reports/ji/4jii | HTTPS FTP |
-Related structure data
Related structure data | 4gqgSC 4i5xC 4jihC 4jirC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36297.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B10, AKR1B11 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 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-ZST / |
#4: Chemical | ChemComp-NA / |
#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: 2.53 Å3/Da / Density % sol: 51.39 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 30-35% (w/v) PEG 6000 and 100 mM Tris-base (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: Dec 27, 2012 | ||||||||||||||||||
Radiation | Monochromator: Multilayer Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.2→25.98 Å / Num. all: 18446 / Num. obs: 18428 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 28.163 Å2 / Rmerge(I) obs: 0.091 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GQG Resolution: 2.2→24.667 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→24.667 Å
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Refine LS restraints |
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LS refinement shell |
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