+Open data
-Basic information
Entry | Database: PDB / ID: 4gqg | ||||||
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Title | Crystal structure of AKR1B10 complexed with NADP+ | ||||||
Components | Aldo-keto reductase family 1 member B10 | ||||||
Keywords | OXIDOREDUCTASE / alpha-beta TIM barrel / NADP-dependant oxidoreductase / NADP+ | ||||||
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: 1.92 Å | ||||||
Authors | Zhang, L. / Zheng, X. / Chen, S. / Zhai, J. / Hu, X. | ||||||
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 | 4gqg.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gqg.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 4gqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gqg_validation.pdf.gz | 713.1 KB | Display | wwPDB validaton report |
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Full document | 4gqg_full_validation.pdf.gz | 715.7 KB | Display | |
Data in XML | 4gqg_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 4gqg_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/4gqg ftp://data.pdbj.org/pub/pdb/validation_reports/gq/4gqg | HTTPS FTP |
-Related structure data
Related structure data | 4i5xC 4jihC 4jiiC 4jirC 1zuaS S: Starting model for refinement C: citing same article (ref.) |
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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: 36297.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: Human / Gene: AKR1B10 / 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: Water | ChemComp-HOH / |
Sequence details | THIS RESIDUE CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.49 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 100mM Tris, 30-35% PEG6000, 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: Dec 31, 2011 |
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: 1.9→26.03 Å / Num. all: 28056 / Num. obs: 28024 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4074 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZUA Resolution: 1.92→24.515 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.36 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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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 max: 77.17 Å2 / Biso mean: 22.3178 Å2 / Biso min: 8.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→24.515 Å
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LS refinement shell | Resolution: 1.92→1.97 Å / Total num. of bins used: 20
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