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- PDB-8dr9: Crystal structure of human ALDH2 in complex with NAD+ and PEG MME 550 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dr9 | ||||||
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Title | Crystal structure of human ALDH2 in complex with NAD+ and PEG MME 550 | ||||||
![]() | Aldehyde dehydrogenase, mitochondrial | ||||||
![]() | OXIDOREDUCTASE / ALDH2 / aldehyde dehydrogenase / mitochondrial | ||||||
Function / homology | ![]() Metabolism of serotonin / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / aldehyde catabolic process / phenylacetaldehyde dehydrogenase (NAD+) activity / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation ...Metabolism of serotonin / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / aldehyde catabolic process / phenylacetaldehyde dehydrogenase (NAD+) activity / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation / carboxylesterase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / Smooth Muscle Contraction / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / electron transfer activity / mitochondrial matrix / mitochondrion / extracellular exosome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Xu, S.Y. / Weng, J.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of human ALDH2 in complex with NAD+ and PEG MME 550 Authors: Xu, S.Y. / Weng, J.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.1 KB | Display | ![]() |
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PDB format | ![]() | 183 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
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Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 48.5 KB | Display | |
Data in CIF | ![]() | 72 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vleS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 54540.621 Da / Num. of mol.: 2 / Mutation: C302S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 956 molecules ![](data/chem/img/CIT.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-1PE / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.94 % / Description: 3D |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: protein conditions: 8 mg/ml recombinant ALDH2 in 20 mM Tris-HCl, pH 8.0, 50 mM NaCl, 1 mM DTT, supplemented with 2-4% v/v DMSO well conditions: 100 mM sodium citrate, pH 5.0-5.6, 22-26% w/v ...Details: protein conditions: 8 mg/ml recombinant ALDH2 in 20 mM Tris-HCl, pH 8.0, 50 mM NaCl, 1 mM DTT, supplemented with 2-4% v/v DMSO well conditions: 100 mM sodium citrate, pH 5.0-5.6, 22-26% w/v PEG MME 550 550 hanging drops were set with a 1.5:1 protein:well ratio PH range: 5.0-5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→49.92 Å / Num. obs: 155768 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.999 / Net I/σ(I): 16.37 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 13.7 % / Num. unique obs: 24827 / CC1/2: 0.809 / % possible all: 99.6 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2VLE Resolution: 1.5→49.92 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.111 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 88.33 Å2 / Biso mean: 15.868 Å2 / Biso min: 4.89 Å2
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Refinement step | Cycle: final / Resolution: 1.5→49.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.504→1.543 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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