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- PDB-1qv6: HORSE LIVER ALCOHOL DEHYDROGENASE HIS51GLN/LYS228ARG MUTANT COMPL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qv6 | ||||||
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Title | HORSE LIVER ALCOHOL DEHYDROGENASE HIS51GLN/LYS228ARG MUTANT COMPLEXED WITH NAD+ AND 2,4-DIFLUOROBENZYL ALCOHOL | ||||||
![]() | Alcohol dehydrogenase E chain | ||||||
![]() | OXIDOREDUCTASE / DEHYDROGENASE / ALCOHOL / NICOTINAMIDE COENZYME / 2 / 4-DIFLUOROBENZYL ALCOHOL / HIS51GLN/LYS228ARG MUTANT / HORSE LIVER | ||||||
Function / homology | ![]() : / : / 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 | ![]() ![]() ![]() | ||||||
![]() | Lebrun, L.A. / Park, D.-H. / Ramaswamy, S. / Plapp, B.V. | ||||||
![]() | ![]() Title: Participation of histidine-51 in catalysis by horse liver alcohol dehydrogenase. Authors: LeBrun, L.A. / Park, D.-H. / Ramaswamy, S. / Plapp, B.V. #1: ![]() Title: Structures of Liver Alcohol Dehydrogenase Complexed with Nad+ and Substituted Benzyl Alcohols. Authors: Ramaswamy, S. / Eklund, H. / Plapp, B.V. #2: ![]() Title: Control of Coenzyme Binding to Horse Liver Alcohol Dehydrogenase. Authors: LeBrun, L.A. / Plapp, B.V. #3: ![]() Title: Mobility of Fluorobenzyl Alcohols Bound to Liver Alcohol Dehydrogenase as Determined by NMR and X-Ray Crystallographic Studies. Authors: Rubach, J.K. / Plapp, B.V. #4: ![]() Title: Structure of a Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 A Resolution Authors: Eklund, H. / Samama, J.P. / Wallen, L. / Branden, C.I. / Akeson, A. / Jones, T.A. #5: ![]() Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 A Resolution Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A. #6: ![]() Title: Binding of Substrate in a Ternary Complex of Horse Liver Alcohol Dehydrogenase Authors: Eklund, H. / Plapp, B.V. / Samama, J.-P. / Branden, C.-I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.2 KB | Display | ![]() |
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PDB format | ![]() | 130.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 986.7 KB | Display | ![]() |
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Full document | ![]() | 991.2 KB | Display | |
Data in XML | ![]() | 33.5 KB | Display | |
Data in CIF | ![]() | 50.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qv7C ![]() 1hldS 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: 39871.270 Da / Num. of mol.: 2 / Fragment: Recombinant without the wild-type N-acetyl group / Mutation: H51Q and K228R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 588 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/24B.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/24B.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.58 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: dialysis / pH: 7 Details: 50 mM ammonium N-[tris(hydroxymethyl)methyl)]-2-aminoethanesulfonate buffer, 1 mM NAD+, 10 mM 2,4-difluorobenzyl alcohol, 2-methyl-2,4-pentanediol, pH 7.0, dialysis, temperature 278K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 5 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 11, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9315 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. all: 63963 / Num. obs: 63963 / % possible obs: 93.3 % / Redundancy: 1.94 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.3 / Num. unique all: 4402 / % possible all: 93.6 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. measured all: 124354 |
Reflection shell | *PLUS % possible obs: 93.6 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HLD Resolution: 1.8→10 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.701 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.12
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.556 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.845 Å / Total num. of bins used: 20 /
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Software | *PLUS Version: 5 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.203 / Rfactor Rwork: 0.157 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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