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- PDB-4l2o: Crystal structure of human ALDH3A1 with its selective inhibitor 1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4l2o | ||||||
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Title | Crystal structure of human ALDH3A1 with its selective inhibitor 1-(4-fluorophenyl)sulfonyl-2-methylbenzimidazole | ||||||
![]() | Aldehyde dehydrogenase | ||||||
![]() | OXIDOREDUCTASE/Inhibitor / Catalyzes benzaldehyde / Rossmann fold / Dehydrogenase / NADP+ binding / OXIDOREDUCTASE-Inhibitor complex | ||||||
Function / homology | ![]() aldehyde dehydrogenase [NAD(P)+] / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / aldehyde dehydrogenase [NAD(P)+] activity / cellular aldehyde metabolic process / aldehyde dehydrogenase (NAD+) activity / Phase I - Functionalization of compounds / xenobiotic metabolic process / lipid metabolic process ...aldehyde dehydrogenase [NAD(P)+] / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / aldehyde dehydrogenase [NAD(P)+] activity / cellular aldehyde metabolic process / aldehyde dehydrogenase (NAD+) activity / Phase I - Functionalization of compounds / xenobiotic metabolic process / lipid metabolic process / endoplasmic reticulum / extracellular space / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hurley, T.D. / Parajuli, B. | ||||||
![]() | ![]() Title: Crystal structure of human ALDH3A1 with its selective inhibitor 1-(4-fluorophenyl)sulfonyl-2-methylbenzimidazole Authors: Parajuli, B. / Hurley, T.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 376.4 KB | Display | ![]() |
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PDB format | ![]() | 305.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 72.9 KB | Display | |
Data in CIF | ![]() | 102.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3szaS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABEG
#1: Protein | Mass: 52245.738 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P30838, aldehyde dehydrogenase [NAD(P)+] |
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-Non-polymers , 5 types, 927 molecules ![](data/chem/img/K.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/1DD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/1DD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-K / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-NAD / #5: Chemical | ChemComp-1DD / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Potassium acetate, 20% PEG 3350, (4 microlitres of 4 mg/mL of ALDH3A1 + 4 microlitres of mother liquor), 1 mM NAD+, 1 mM compound solution, 1 DMSO, pH 7.5, VAPOR DIFFUSION, SITTING ...Details: 0.2 M Potassium acetate, 20% PEG 3350, (4 microlitres of 4 mg/mL of ALDH3A1 + 4 microlitres of mother liquor), 1 mM NAD+, 1 mM compound solution, 1 DMSO, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 27, 2013 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9869 Å / Relative weight: 1 |
Reflection | Resolution: 1.937→50 Å / Num. all: 132178 / Num. obs: 127287 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.34 / Rsym value: 0.072 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.937→1.98 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.5 / Num. unique all: 6331 / % possible all: 92.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3SZA Resolution: 1.937→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.411 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 32.032 Å2
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Refinement step | Cycle: LAST / Resolution: 1.937→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.937→1.987 Å / Total num. of bins used: 20
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