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Yorodumi- PDB-5vn1: horse liver alcohol dehydrogenae complexed with NADH (R,S)-N-1-me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vn1 | |||||||||
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Title | horse liver alcohol dehydrogenae complexed with NADH (R,S)-N-1-methylhexylformamide | |||||||||
Components | Alcohol dehydrogenase E chain | |||||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase / horse liver / NADH N-1-methylhexylformamide | |||||||||
Function / homology | Function and homology information : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinol metabolic process / retinoic acid metabolic process / zinc ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Equus caballus (horse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | |||||||||
Authors | Plapp, B.V. / Ramaswamy, S. / Ferraro, D.J. / Baskar Raj, S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochemistry / Year: 2017 Title: Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. Authors: Plapp, B.V. / Savarimuthu, B.R. / Ferraro, D.J. / Rubach, J.K. / Brown, E.N. / Ramaswamy, S. #1: Journal: Biochemistry / Year: 2012 Title: Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes. Authors: Plapp, B.V. / Ramaswamy, S. #2: Journal: J. Biol. Chem. / Year: 2003 Title: Formamides mimic aldehydes and inhibit liver alcohol dehydrogenases and ethanol metabolism. Authors: Venkataramaiah, T.H. / Plapp, B.V. #3: Journal: Biochemistry / Year: 1997 Title: Flexibility of liver alcohol dehydrogenase in stereoselective binding of 3-butylthiolane 1-oxides. Authors: Cho, H. / Ramaswamy, S. / Plapp, B.V. #4: Journal: Biochemistry / Year: 1997 Title: Binding of formamides to liver alcohol dehydrogenase. Authors: Ramaswamy, S. / Scholze, M. / Plapp, B.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vn1.cif.gz | 621.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vn1.ent.gz | 511.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vn1_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5vn1_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5vn1_validation.xml.gz | 67.8 KB | Display | |
Data in CIF | 5vn1_validation.cif.gz | 99.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/5vn1 ftp://data.pdbj.org/pub/pdb/validation_reports/vn/5vn1 | HTTPS FTP |
-Related structure data
Related structure data | 5vj5C 5vjgC 5vkrC 5vl0C 1p1rS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 39853.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase |
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-Non-polymers , 6 types, 1340 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAI / #4: Chemical | ChemComp-NWH / #5: Chemical | #6: Chemical | ChemComp-NMH / ( | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.22 % / Description: long block |
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Crystal grow | Temperature: 278 K / Method: microdialysis / pH: 7 Details: 10 mg protein/ml dialyzed against 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonate buffer, pH 7 (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM (racemic) (R,S)-N-1- ...Details: 10 mg protein/ml dialyzed against 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonate buffer, pH 7 (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM (racemic) (R,S)-N-1-methylhexylformamide as the concentration of 2-methyl-2,4-pentanediol was raised to 25%. Crystal on loop plunged into liquid N2. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.936 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 1, 1999 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.936 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→20 Å / Num. obs: 386016 / % possible obs: 83.8 % / Observed criterion σ(I): -3 / Redundancy: 1.762 % / Rmerge F obs: 0.13 / Rmerge(I) obs: 0.122 / Rrim(I) all: 0.151 / Net I/σ(I): 5.77 / Num. measured all: 680160 / Scaling rejects: 57 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1p1r Resolution: 1.25→20 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.431 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.05 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.95 Å2 / Biso mean: 25.461 Å2 / Biso min: 15.64 Å2
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Refinement step | Cycle: final / Resolution: 1.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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