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Yorodumi- PDB-8fh5: Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NAD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fh5 | ||||||
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Title | Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-001 | ||||||
Components | Aldo-keto reductase family 1 member B1 | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / COMPLEX / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase (NADP+) activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase (NADP+) activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / L-ascorbic acid biosynthetic process / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / daunorubicin metabolic process / doxorubicin metabolic process / epithelial cell maturation / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / carbohydrate metabolic process / electron transfer activity / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Arenas, R. / Wilson, D.K. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-001 Authors: Arenas, R. / Wilson, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fh5.cif.gz | 142.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fh5.ent.gz | 106.7 KB | Display | PDB format |
PDBx/mmJSON format | 8fh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fh5_validation.pdf.gz | 998.7 KB | Display | wwPDB validaton report |
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Full document | 8fh5_full_validation.pdf.gz | 1001.8 KB | Display | |
Data in XML | 8fh5_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 8fh5_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/8fh5 ftp://data.pdbj.org/pub/pdb/validation_reports/fh/8fh5 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35767.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1, ALR2 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P15121, NADP-retinol dehydrogenase, D/L-glyceraldehyde reductase, allyl-alcohol dehydrogenase, aldose reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-XXQ / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% PEG 3350, 100 mM Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→36.674 Å / Num. obs: 34509 / % possible obs: 88.6 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.042 / Rrim(I) all: 0.059 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.62→1.65 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.145 / Num. unique obs: 1727 / CC1/2: 0.976 / Rpim(I) all: 0.145 / Rrim(I) all: 0.205 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→36.674 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.171 / WRfactor Rwork: 0.146 / SU B: 1.229 / SU ML: 0.044 / Average fsc free: 0.9824 / Average fsc work: 0.9882 / Cross valid method: FREE R-VALUE / ESU R: 0.087 / ESU R Free: 0.083 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→36.674 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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