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Yorodumi- PDB-8fh6: Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NAD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fh6 | ||||||
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Title | Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And Two AT-001 | ||||||
Components | Aldo-keto reductase family 1 member B1 | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Inhibitor Complex / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
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: 1.952 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 Two 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 | 8fh6.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fh6.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 8fh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fh6_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8fh6_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8fh6_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 8fh6_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/8fh6 ftp://data.pdbj.org/pub/pdb/validation_reports/fh/8fh6 | 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: 35914.340 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 | #4: Chemical | #5: 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: 2.71 Å3/Da / Density % sol: 54.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25%PEG 3,350, 100 mM Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.12709 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12709 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→36.93 Å / Num. obs: 27908 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.037 / Rrim(I) all: 0.087 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4008 / Rpim(I) all: 0.225 / Rrim(I) all: 0.467 / % possible all: 99 |
Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.952→33.719 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.175 / WRfactor Rwork: 0.147 / SU B: 3.34 / SU ML: 0.093 / Average fsc free: 0.9697 / Average fsc work: 0.9811 / Cross valid method: FREE R-VALUE / ESU R: 0.142 / ESU R Free: 0.132 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: 22.923 Å2
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Refinement step | Cycle: LAST / Resolution: 1.952→33.719 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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