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- PDB-8g39: 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: 8g39 | ||||||
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Title | Horse liver alcohol dehydrogense His-51-Gln form complexed with NADH and N-cyclohexylformamide | ||||||
![]() | Alcohol dehydrogenase E chain | ||||||
![]() | OXIDOREDUCTASE / alcohol dehydrogenase horse liver His-51-Gln substitution complex with NADH and N-cyclohexylformamide | ||||||
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 | ![]() | 330.2 KB | Display | ![]() |
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PDB format | ![]() | 266.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 35.6 KB | Display | |
Data in CIF | ![]() | 53.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8g2lC ![]() 8g2sC ![]() 8g2xC ![]() 8g4vC ![]() 1qv6S C: citing same article ( 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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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 , 5 types, 649 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/CXF.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/CXF.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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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45 % / Description: block |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 7 Details: 10 mg/ml protein in 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfate buffer with 0.25 mM EDTA, 1 mM NADH and 15 mM N-cyclohexylformamide, 13 % 2-methyl-2,4- ...Details: 10 mg/ml protein in 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfate buffer with 0.25 mM EDTA, 1 mM NADH and 15 mM N-cyclohexylformamide, 13 % 2-methyl-2,4-pentanediol,raised to 25% MPD before crystal pliunged into liquid N2. |
-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: Feb 4, 2004 / Details: confocal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: grafite / 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→19.9 Å / Num. obs: 121863 / % possible obs: 87.9 % / Redundancy: 2.35 % / Rmerge(I) obs: 0.028 / Rrim(I) all: 0.036 / Χ2: 1.13 / Net I/σ(I): 16 / Num. measured all: 288685 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1qv6 Resolution: 1.42→19.91 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.799 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.28 Å2
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Refinement step | Cycle: 1 / Resolution: 1.42→19.91 Å
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Refine LS restraints |
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