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- PDB-6o91: Horse liver L57F alcohol dehydrogenase complexed with NAD and pen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6o91 | |||||||||
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Title | Horse liver L57F alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol | |||||||||
![]() | Alcohol dehydrogenase E chain | |||||||||
![]() | OXIDOREDUCTASE / alcohol dehydrogenase / NAD / pentafluorobenzyl alcohol / Leu57 to Phe57 substitution / Horse liver E enzyme | |||||||||
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: Substitutions of Amino Acid Residues in the Substrate Binding Site of Horse Liver Alcohol Dehydrogenase Have Small Effects on the Structures but Significantly Affect Catalysis of Hydrogen Transfer. Authors: Kim, K. / Plapp, B.V. #1: Journal: Biochemistry / Year: 1993 Title: Unmasking of hydrogen tunneling in the horse liver alcohol dehydrogenase reaction by site-directed mutagenesis. Authors: Bahnson, B.J. / Park, D.H. / Kim, K. / Plapp, B.V. / Klinman, J.P. #2: ![]() Title: Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes. Authors: Plapp, B.V. / Ramaswamy, S. #3: ![]() Title: Catalysis by Alcohol Dehydrogenases Authors: Plapp, B.V. #4: ![]() Title: Inversion of substrate stereoselectivity of horse liver alcohol dehydrogenase by substitutions of Ser-48 and Phe-93. Authors: Kim, K. / 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 | ![]() | 361.1 KB | Display | ![]() |
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PDB format | ![]() | 292.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 970.5 KB | Display | ![]() |
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Full document | ![]() | 971.6 KB | Display | |
Data in XML | ![]() | 40.5 KB | Display | |
Data in CIF | ![]() | 64.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oa7C ![]() 6owmC ![]() 6owpC ![]() 4dwvS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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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: 39887.289 Da / Num. of mol.: 2 / Mutation: L57F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1118 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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-Details
Nonpolymer details | NAJ is the dianionic form of NAD, refined with relaxed restraints on the nicotinamide ring |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.96 % / 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 / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2007 / Details: ADJUSTABLE FOCUS K-B PAIR SIPLUS PT, RH COATINGS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL CRYOCOOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.09→19.89 Å / Num. obs: 273671 / % possible obs: 88 % / Redundancy: 5.52 % / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.113 / Χ2: 1.17 / Net I/σ(I): 10 / Num. measured all: 1521595 / Scaling rejects: 11412 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DWV Resolution: 1.1→19.9 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.74 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.025 / 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: 66.83 Å2 / Biso mean: 15.169 Å2 / Biso min: 7.58 Å2
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Refinement step | Cycle: final / Resolution: 1.1→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.128 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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