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Open data
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Basic information
Entry | Database: PDB / ID: 6xt2 | ||||||
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Title | EQADH-NADH-HEPTAFLUOROBUTANOL, P21 | ||||||
![]() | Alcohol dehydrogenase E chain | ||||||
![]() | OXIDOREDUCTASE / alcohol dehydrogenase / NADH / horse liver | ||||||
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. / Ramaswamy, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Alternative binding modes in abortive NADH-alcohol complexes of horse liver alcohol dehydrogenase. Authors: Plapp, B.V. / Subramanian, R. #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: Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. Authors: Plapp, B.V. / Savarimuthu, B.R. / Ferraro, D.J. / Rubach, J.K. / Brown, E.N. / Ramaswamy, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 626.5 KB | Display | ![]() |
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PDB format | ![]() | 519.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.8 MB | Display | ![]() |
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Full document | ![]() | 3.8 MB | Display | |
Data in XML | ![]() | 69.1 KB | Display | |
Data in CIF | ![]() | 100.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jqaC ![]() 7k35C ![]() 5vl0S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 1237 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/B7F.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/B7F.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAI / #4: Chemical | ChemComp-B7F / #5: Chemical | #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: 2.24 Å3/Da / Density % sol: 48.12 % |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 7 Details: 10 mg/ml protein, 1 mM NAD+, 4 mM 1H,1H-heptafluorobutanol, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethananesulfonate, 10-25% 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: RIGAKU / Detector: AREA DETECTOR / Date: Apr 12, 2004 / Details: confocal | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→19.92 Å / Num. obs: 188871 / % possible obs: 88.3 % / Redundancy: 5.64 % / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.053 / Χ2: 1.13 / Net I/σ(I): 20.7 / Num. measured all: 1072997 / Scaling rejects: 8048 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5VL0 Resolution: 1.55→19.84 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.501 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.082 / 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: 82.28 Å2 / Biso mean: 20.908 Å2 / Biso min: 10.32 Å2
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Refinement step | Cycle: final / Resolution: 1.55→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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