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- PDB-7adh: THREE-DIMENSIONAL STRUCTURE OF ISONICOTINIMIDYLATED LIVER ALCOHOL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7adh | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF ISONICOTINIMIDYLATED LIVER ALCOHOL DEHYDROGENASE | ||||||
![]() | ISONICOTINIMIDYLATED LIVER ALCOHOL DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE (NAD(A)-CHOH(D)) | ||||||
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 | ![]() | ||||||
![]() | Plapp, B. / Eklund, H. | ||||||
![]() | ![]() Title: Three-dimensional structure of isonicotinimidylated liver alcohol dehydrogenase. Authors: Plapp, B.V. / Eklund, H. / Jones, T.A. / Branden, C.I. #1: ![]() Title: Interdomain Motion in Liver Alcohol Dehydrogenase. Structural and Energetic Analysis of the Hinge Bending Mode Authors: Colonna-Cesari, F. / Perahia, D. / Karplus, M. / Eklund, H. / Branden, C.I. / Tapia, O. #2: ![]() Title: Crystallographic Investigations of Nicotinamide Adenine Dinucleotide Binding to Horse Liver Alcohol Dehydrogenase Authors: Eklund, H. / Samama, J.-P. / Jones, T.A. #3: ![]() Title: Crystal Structures of the Active Site in Specifically Metal-Depleted and Cobalt-Substituted Horse Liver Alcohol Dehydrogenase Derivatives Authors: Schneider, G. / Eklund, H. / Cedergren-Zeppezauer, E. / Zeppezauer, M. #4: ![]() Title: Crystal-Structure Determination of Reduced Nicotinamide Adenine Dinucleotide Complex with Horse Liver Alcohol Dehydrogenase Maintained in its Apo Conformation by Zinc-Bound Imidazole Authors: Cedergren-Zeppezauer, E. #5: ![]() 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. #6: ![]() Title: Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogeanse. Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4-(N,N- ...Title: Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogeanse. Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4-(N,N-Dimethylamino)Cinnamaldehyde to the Enzyme Authors: Cedergren-Zeppezauer, E. / Samama, J.-P. / Eklund, H. #7: ![]() Title: Pyrazole Binding in Crystalline Binary and Ternary Complexes with Liver Alcohol Dehydrogenase Authors: Eklund, H. / Samama, J.-P. / Wallen, L. #8: ![]() Title: Structure of Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 Angstroms Resolution Authors: Eklund, H. / Samama, J.-P. / Wallen, L. / Branden, C.-I. / Akeson, A. / Jones, T.A. #9: ![]() Title: 5-Methylnicotinamide-Adenine Dinucleotide. Kinetic Investigation with Major and Minor Isoenzymes of Liver Alcohol Dehydrogenase and Structural Determination of its Binary Complex with Alcohol Dehydrogenase Authors: Samama, J.-P. / Wrixon, A.D. / Biellmann, J.-F. #10: ![]() Title: Structural Differences between Apo-and Holoenzyme of Horse Liver Alcohol Dehydrogenase Authors: Eklund, H. / Branden, C.-I. #11: ![]() Title: X-Ray Studies of the Binding of Cibacron Blue F3Ga to Liver Alcohol Dehydrogenase Authors: Biellmann, J.-F. / Samama, J.-P. / Branden, C.I. / Eklund, H. #12: ![]() Title: Crystallography of Liver Alcohol Dehydrogenase Complexed with Substrates Authors: Plapp, B.V. / Eklund, H. / Branden, C.-I. #13: ![]() Title: Crystallization of Liver Alcohol Denydrogenase Activated by the Modification of Amino Groups Authors: Plapp, B.V. / Zeppezauer, E. / Branden, C.-I. #14: ![]() Title: Subunit Conformation of Yeast Alcohol Dehydrogenase Authors: Jornvall, H. / Eklund, H. / Branden, C.-I. #15: ![]() Title: The Crystal Structure of Complexes between Horse Liver Alcohol Dehydrogenase and the Coenzyme Analogues 3-Iodopyridine-Adenine Dinucleotide and Pyridine-Adenine Dinucleotide Authors: Samama, J.-P. / Zeppezauer, E. / Biellmann, J.-F. / Branden, C.-I. #16: ![]() Title: X-Ray Investigation of the Binding of 1,10-Phenanthroline and Imidazole to Horse-Liver Alcohol Dehydrogenase Authors: Boiwe, T. / Branden, C.-I. #17: ![]() 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. #18: ![]() Title: Structural Comparisons of Mammalian, Yeast and Bacillar Alcohol Dehydrogenases Authors: Eklund, H. / Branden, C.-I. / Jornvall, H. #19: ![]() Year: 1975 Title: The Binding of Nucleotides to Horse Liver Alcohol Dehydrogenase Authors: Nordstrom, B. / Branden, C.-I. #20: ![]() Title: Alcohol Dehydrogenases Authors: Branden, C.-I. / Jornvall, H. / Eklund, H. / Furugren, B. #21: ![]() Title: The Conformation of Adenosine Diphosphoribose and 8-Bromoadenosine Diphosphoribose When Bound to Liver Alcohol Dehydrogenase Authors: Abdallah, M.A. / Biellmann, J.-F. / Nordstrom, B. / Branden, C.-I. #22: ![]() Title: The Structure of Horse Liver Alcohol Dehydrogenase Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Branden, C.-I. #23: ![]() Title: Structural and Functional Similarities within the Coenzyme Binding Domains of Dehydrogenases Authors: Ohlsson, I. / Nordstrom, B. / Branden, C.-I. #24: ![]() Title: Binding of Salicylate in the Adenosine-Binding Pocket of Dehydrogenases Authors: Einarsson, R. / Eklund, H. / Zeppezauer, E. / Boiwe, T. / Branden, C.-I. #25: ![]() Title: Structure of Liver Alcohol Dehydrogenase at 2.9-Angstroms Resolution Authors: Branden, C.-I. / Eklund, H. / Nordstrom, B. / Boiwe, T. / Soderlund, G. / Zeppezauer, E. / Ohlsson, I. / Akeson, A. #26: ![]() Title: Structure of Horse Liver Alcohol Dehydrogenase. I. Structural Symmetry and Conformational Changes Authors: Branden, C.-I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 88.3 KB | Display | ![]() |
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PDB format | ![]() | 60.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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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Atom site foot note | 1: RESIDUE 62 IS A CIS-PROLINE. 2: THIS ATOM WAS NOT LOCATED IN THE ELECTRON DENSITY MAP. COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA. 3: SEE REMARK 5. / 4: SEE FTNOTE 2 AND REMARK 5. |
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Components
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#2: Chemical | #3: Chemical | ChemComp-NTN / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67.11 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 5 ℃ / pH: 8.3 / Method: microdialysisDetails: first dialysised against R1 solution and then against R2 solution. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 3.2 Å / Num. obs: 10091 |
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Processing
Software | Name: CORELS / Classification: refinement | ||||||||||||
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Refinement | Rfactor obs: 0.29 / Highest resolution: 3.2 Å Details: IN THIS STRUCTURE MOST OF THE LYSINE RESIDUES WERE AMIDINATED WITH METHYL ISONICOTINIMIDATE. THE DETERMINATION OF WHICH LYSINE RESIDUES WERE MODIFIED AND THEIR SEPARATION INTO CLASSES WAS ...Details: IN THIS STRUCTURE MOST OF THE LYSINE RESIDUES WERE AMIDINATED WITH METHYL ISONICOTINIMIDATE. THE DETERMINATION OF WHICH LYSINE RESIDUES WERE MODIFIED AND THEIR SEPARATION INTO CLASSES WAS BASED ON THE ELECTRON DENSITY MAP. THE FOLLOWING LYSINES WERE MODIFIED - 10, 18, 19, 39, 88, 99, 113, 135, 159, 168, 185, 188, 212, 228, 231, 247, 325, 330, 354. THE FOLLOWING LYSINES WERE PROBABLY MODIFIED - 5, 8, 32, 226. THE FOLLOWING LYSINES WERE NOT MODIFIED OR UNCERTAIN - 104, 223, 248, 315, 323, 338, 339. | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.2 Å
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Refinement | *PLUS Highest resolution: 3.2 Å / Rfactor obs: 0.29 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |