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- PDB-8g2l: Horse liver alcohol dehydrogense His-51 Gln form complexed with N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8g2l | ||||||
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Title | Horse liver alcohol dehydrogense His-51 Gln form complexed with NAD+ and 2,2,2-trifluoroethanol | ||||||
![]() | Alcohol dehydrogenase E chain | ||||||
![]() | OXIDOREDUCTASE / alcohol dehydrogenase horse liver His-48 Gln substitution complex with NAD+ and trifluoroethanol | ||||||
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: Histidine-51 facilitates deprotonation of the zinc-bound ligand during catalysis by horse liver alcohol dehydrogenase Authors: Plapp, B.V. / Kovaleva, E.G. #1: ![]() Title: Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes. Authors: Plapp, B.V. / Ramaswamy, S. #2: ![]() Title: Participation of histidine-51 in catalysis by horse liver alcohol dehydrogenase. Authors: LeBrun, L.A. / Park, D.H. / Ramaswamy, S. / Plapp, B.V. #3: ![]() Title: Proton Transfer In The Mechanism Of Horse Liver Alcohol Dehydrogenase Authors: Kovaleva, E.G. #4: Journal: Biochemistry / Year: 1999 Title: Control of coenzyme binding to horse liver alcohol dehydrogenase. Authors: Plapp, B.V. / LeBrun, L.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.5 KB | Display | ![]() |
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PDB format | ![]() | 137.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.5 MB | Display | ![]() |
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Full document | ![]() | 4.5 MB | Display | |
Data in XML | ![]() | 36.5 KB | Display | |
Data in CIF | ![]() | 55.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8g2sC ![]() 8g2xC ![]() 8g39C ![]() 8g4vC C: citing same article ( |
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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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39843.258 Da / Num. of mol.: 2 / Mutation: H51Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 678 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NAJ.gif)
![](data/chem/img/ETF.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAJ.gif)
![](data/chem/img/ETF.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MRD / ( | #7: 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: 2.26 Å3/Da / Density % sol: 45 % / Description: block |
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Crystal grow | Temperature: 278 K / Method: batch mode / pH: 7 Details: 10 mg/ml protein, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminiomethanesulfonate and 0.25 mM EDTA, 2 mM NAD+, 0.1 mM 2,2,2-trifluoroetanol, 13% MPD, crystals soaked with 25% MPD, and ...Details: 10 mg/ml protein, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminiomethanesulfonate and 0.25 mM EDTA, 2 mM NAD+, 0.1 mM 2,2,2-trifluoroetanol, 13% MPD, crystals soaked with 25% MPD, and 100 mM trifluoroethanol Temp details: oH 6,7 at 298 K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 24, 2004 / Details: confocal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: graphie / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.42→19.87 Å / Num. obs: 121088 / % possible obs: 87.2 % / Redundancy: 6.16 % / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Χ2: 1.18 / Net I/σ(I): 17.2 / Num. measured all: 751297 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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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: 21.355 Å2
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Refinement step | Cycle: 1 / Resolution: 1.42→19.88 Å
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Refine LS restraints |
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