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- PDB-5kje: F322L horse liver alcohol dehydrogenase complexed with NAD+ and p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kje | ||||||
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Title | F322L horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol | ||||||
![]() | Alcohol dehydrogenase E chain | ||||||
![]() | OXIDOREDUCTASE / Rossmann fold / Michaelis analogue / dynamics | ||||||
Function / homology | ![]() alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinol metabolic process / retinoic acid metabolic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Plapp, B.V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis. Authors: Shanmuganatham, K.K. / Wallace, R.S. / Ting-I Lee, A. / Plapp, B.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 345.2 KB | Display | ![]() |
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PDB format | ![]() | 279 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 986 KB | Display | ![]() |
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Full document | ![]() | 989.5 KB | Display | |
Data in XML | ![]() | 39.1 KB | Display | |
Data in CIF | ![]() | 61.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cdgC ![]() 5cdsC ![]() 5cdtC ![]() 5cduC ![]() 5kj6C ![]() 5kjcC ![]() 5kjfC ![]() 4dwvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39819.258 Da / Num. of mol.: 2 / Mutation: F322L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 984 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NAJ.gif)
![](data/chem/img/PFB.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAJ.gif)
![](data/chem/img/PFB.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MRD / ( #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: 46 % / Description: block |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 7 Details: 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL) METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 10 MM 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: NOIR-1 / Detector: CCD / Date: Apr 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8865 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→20 Å / Num. obs: 166162 / % possible obs: 82.8 % / Redundancy: 3.34 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.26→1.31 Å / Redundancy: 3.11 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.4 / % possible all: 51.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DWV Resolution: 1.26→20 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.301 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.04 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.072 Å2
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Refinement step | Cycle: 1 / Resolution: 1.26→20 Å
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Refine LS restraints |
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