+Open data
-Basic information
Entry | Database: PDB / ID: 1ye3 | ||||||
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Title | HORSE LIVER ALCOHOL DEHYDROGENASE APOENZYME | ||||||
Components | Alcohol dehydrogenase E chain | ||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE / ALCOHOL / LIVER / APOENZYME / METHYLPENTANEDIOL | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Plapp, B.V. / Savarimuthu, B.R. / Ramaswamy, S. | ||||||
Citation | Journal: To be Published Title: Horse Liver Alcohol Dehydrogenase Apoenzyme Authors: Plapp, B.V. / Savarimuthu, B.R. / Ramaswamy, S. #1: 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. #2: Journal: J.Mol.Biol. / Year: 1981 Title: Structure of a 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. / A Jones, T. #3: Journal: Biochemistry / Year: 1999 Title: Substitutions in the Flexible Loop of Horse Liver Alcohol Dehydrogenase Hinder the Conformational Change and Unmask Hydrogen Transfer Authors: Ramaswamy, S. / Park, D.H. / Plapp, B.V. #4: Journal: Biochemistry / Year: 2001 Title: Contributions of Valine-292 in the Nicotinamide Binding Site of Liver Alcohol Dehydrogenase and Dynamics to Catalysis Authors: Rubach, J.K. / Ramaswamy, S. / Plapp, B.V. #5: 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. #6: Journal: Biochemistry / Year: 1994 Title: Structures of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Substituted Benzyl Alcohols Authors: Ramaswamy, S. / Eklund, H. / Plapp, B.V. #7: Journal: Biochemistry / Year: 2002 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. #8: Journal: Biochemistry / Year: 2003 Title: Amino Acid Residues in the Nicotinamide Binding Site Contribute to Catalysis by Horse Liver Alcohol Dehydrogenase Authors: Rubach, J.K. / Plapp, B.V. #9: 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. #10: Journal: Biochemistry / Year: 1982 Title: Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogenase. 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 Dehydrogenase. 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ye3.cif.gz | 153.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ye3.ent.gz | 120 KB | Display | PDB format |
PDBx/mmJSON format | 1ye3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/1ye3 ftp://data.pdbj.org/pub/pdb/validation_reports/ye/1ye3 | HTTPS FTP |
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-Related structure data
Related structure data | 8adhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: liver / Source: (natural) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase | ||||
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#2: Chemical | #3: Chemical | ChemComp-MPD / ( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.79 % |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 8.4 Details: 50 mM Tris-HCl, 25% methylpentanediol, pH 8.4, MICRODIALYSIS, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→20.2 Å / Num. obs: 36732 / % possible obs: 71.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.66 % / Biso Wilson estimate: 25.468 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.59→1.65 Å / Redundancy: 5.74 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2918 / % possible all: 58 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8ADH Resolution: 1.59→20.2 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.926 / SU ML: 0.069 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.2 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Positions for residues A269-A270 were not well-defined by the electron density. Several residues, including A306, have alternative conformations, but these were not modeled.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→20.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.631 Å / Total num. of bins used: 20
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