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Open data
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Basic information
Entry | Database: PDB / ID: 1mgo | ||||||
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Title | Horse Liver Alcohol Dehydrogenase Phe93Ala Mutant | ||||||
![]() | Alcohol Dehydrogenase E chain | ||||||
![]() | OXIDOREDUCTASE / Dehydrogenase / Alcohol / Nicotinamide Coenzyme / Mutant / Substrate binding site | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Rubach, J.K. / Plapp, B.V. | ||||||
![]() | ![]() Title: Mobility of Fluorobenzyl Alcohols Bound to Liver Alcohol Dehydrogenases as Determined by NMR and X-ray Crystallographic Studies Authors: Rubach, J.K. / Plapp, B.V. #1: ![]() Title: Structures of Horse Liver Alcohol Dehydrogenase Complexed with NAD+ and Substituted Benzyl Alcohols. Authors: Ramaswamy, S. / Eklund, H. / Plapp, B.V. #2: ![]() 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. #3: ![]() Title: Structure of a Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 Angstrom Resolution Authors: Eklund, H. / Samma, J.P. / Wallen, L. / Branden, C.I. / Akeson, A. / Jones, T.A. #4: ![]() Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 Angstroms Resolution Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE BIOLOGICALLY ACTIVE DIMERIC MOLECULE AB (2 CHAINS). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 293.4 KB | Display | ![]() |
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PDB format | ![]() | 235.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1mg0C ![]() 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: 39777.180 Da / Num. of mol.: 2 / Mutation: F93A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 474 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/PFB.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/PFB.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: 2.42 Å3/Da / Density % sol: 49.18 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: dialysis / pH: 7 / Details: MPD, pH 7.0, Dialysis, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 253 ℃ / pH: 6.7 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.2→20 Å / Num. obs: 199442 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.25 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 5.3 | ||||||||||||||||||
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 1.46 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.29 / % possible all: 84.5 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 86.6 % / Num. measured all: 455785 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 84.5 % / Rmerge(I) obs: 0.29 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HLD Resolution: 1.2→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.046 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.199 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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