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Yorodumi- PDB-6adh: STRUCTURE OF TRICLINIC TERNARY COMPLEX OF HORSE LIVER ALCOHOL DEH... -
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-Basic information
Entry | Database: PDB / ID: 6adh | ||||||
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Title | STRUCTURE OF TRICLINIC TERNARY COMPLEX OF HORSE LIVER ALCOHOL DEHYDROGENASE AT 2.9 ANGSTROMS RESOLUTION | ||||||
Components | HOLO-LIVER ALCOHOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE (NAD(A)-CHOH(D)) | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | ||||||
Authors | Eklund, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1981 Title: Structure of a triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9 A resolution. Authors: Eklund, H. / Samma, J.P. / Wallen, L. / Branden, C.I. / Akeson, A. / Jones, T.A. #1: Journal: J.Biol.Chem. / Year: 1986 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: Journal: Biochemistry / Year: 1984 Title: Crystallographic Investigations of Nicotinamide Adenine Dinucleotide Binding to Horse Liver Alcohol Dehydrogenase Authors: Eklund, H. / Samama, J.-P. / Jones, T.A. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983 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: Journal: J.Biol.Chem. / Year: 1983 Title: Three-Dimensional Structure of Isonicotinimidylated Liver Alcohol Dehydrogenase Authors: Plapp, B.V. / Eklund, H. / Jones, T.A. / Branden, C.-I. #5: Journal: Biochemistry / Year: 1983 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. #6: Journal: J.Biol.Chem. / Year: 1982 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. #7: Journal: Biochemistry / Year: 1982 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. #8: Journal: Biochemistry / Year: 1982 Title: Pyrazole Binding in Crystalline Binary and Ternary Complexes with Liver Alcohol Dehydrogenase Authors: Eklund, H. / Samama, J.-P. / Wallen, L. #9: Journal: Eur.J.Biochem. / Year: 1981 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: Journal: J.Biol.Chem. / Year: 1979 Title: Structural Differences between Apo-and Holoenzyme of Horse Liver Alcohol Dehydrogenase Authors: Eklund, H. / Branden, C.-I. #11: Journal: Eur.J.Biochem. / Year: 1979 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: Journal: J.Mol.Biol. / Year: 1978 Title: Crystallography of Liver Alcohol Dehydrogenase Complexed with Substrates Authors: Plapp, B.V. / Eklund, H. / Branden, C.-I. #13: Journal: J.Mol.Biol. / Year: 1978 Title: Crystallization of Liver Alcohol Denydrogenase Activated by the Modification of Amino Groups Authors: Plapp, B.V. / Zeppezauer, E. / Branden, C.-I. #14: Journal: J.Biol.Chem. / Year: 1978 Title: Subunit Conformation of Yeast Alcohol Dehydrogenase Authors: Jornvall, H. / Eklund, H. / Branden, C.-I. #15: Journal: Eur.J.Biochem. / Year: 1977 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: Journal: Eur.J.Biochem. / Year: 1977 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: Journal: J.Mol.Biol. / Year: 1976 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: Journal: J.Mol.Biol. / Year: 1976 Title: Structural Comparisons of Mammalian, Yeast and Bacillar Alcohol Dehydrogenases Authors: Eklund, H. / Branden, C.-I. / Jornvall, H. #19: Journal: STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN Year: 1975 Title: The Binding of Nucleotides to Horse Liver Alcohol Dehydrogenase Authors: Nordstrom, B. / Branden, C.-I. #20: Journal: The Enzymes,Third Edition / Year: 1975 Title: Alcohol Dehydrogenases Authors: Branden, C.-I. / Jornvall, H. / Eklund, H. / Furugren, B. #21: Journal: Eur.J.Biochem. / Year: 1975 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: Journal: FEBS Lett. / Year: 1974 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: Journal: J.Mol.Biol. / Year: 1974 Title: Structural and Functional Similarities within the Coenzyme Binding Domains of Dehydrogenases Authors: Ohlsson, I. / Nordstrom, B. / Branden, C.-I. #24: Journal: Eur.J.Biochem. / Year: 1974 Title: Binding of Salicylate in the Adenosine-Binding Pocket of Dehydrogenases Authors: Einarsson, R. / Eklund, H. / Zeppezauer, E. / Boiwe, T. / Branden, C.-I. #25: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973 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: Journal: Arch.Biochem.Biophys. / Year: 1965 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6adh.cif.gz | 135.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6adh.ent.gz | 106.9 KB | Display | PDB format |
PDBx/mmJSON format | 6adh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/6adh ftp://data.pdbj.org/pub/pdb/validation_reports/ad/6adh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUE 62 OF BOTH THE A AND B CHAINS IS A CIS-PROLINE. 2: THIS ATOM WAS NOT LOCATED IN THE ELECTRON DENSITY MAP. COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA. |
-Components
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.53 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.9 Å / Num. obs: 16344 |
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-Processing
Refinement | Highest resolution: 2.9 Å | ||||||||||||
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Refinement step | Cycle: LAST / Highest resolution: 2.9 Å
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Refinement | *PLUS Lowest resolution: 5 Å / Num. reflection obs: 13018 / Rfactor obs: 0.379 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |