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Yorodumi- PDB-1u3t: Crystal Structure of Human Alcohol Dehydrogenase Alpha-Alpha Isof... -
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-Basic information
Entry | Database: PDB / ID: 1u3t | ||||||
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Title | Crystal Structure of Human Alcohol Dehydrogenase Alpha-Alpha Isoform Complexed with N-Cyclopentyl-N-Cyclobutylformamide Determined to 2.5 Angstrom Resolution | ||||||
Components | Alcohol dehydrogenase alpha chain | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information butanol dehydrogenase (NAD+) activity / Abacavir metabolism / alcohol metabolic process / Ethanol oxidation / RA biosynthesis pathway / alcohol dehydrogenase (NAD+) activity / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process ...butanol dehydrogenase (NAD+) activity / Abacavir metabolism / alcohol metabolic process / Ethanol oxidation / RA biosynthesis pathway / alcohol dehydrogenase (NAD+) activity / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Gibbons, B.J. / Hurley, T.D. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Structure of three class I human alcohol dehydrogenases complexed with isoenzyme specific formamide inhibitors Authors: Gibbons, B.J. / Hurley, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u3t.cif.gz | 163.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u3t.ent.gz | 126.8 KB | Display | PDB format |
PDBx/mmJSON format | 1u3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u3t_validation.pdf.gz | 993 KB | Display | wwPDB validaton report |
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Full document | 1u3t_full_validation.pdf.gz | 1009.5 KB | Display | |
Data in XML | 1u3t_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 1u3t_validation.cif.gz | 49.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/1u3t ftp://data.pdbj.org/pub/pdb/validation_reports/u3/1u3t | HTTPS FTP |
-Related structure data
Related structure data | 1u3uC 1u3vC 1u3wC 1hsoS 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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1 |
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Unit cell |
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Details | The assymetric unit contains one homodimer. |
-Components
#1: Protein | Mass: 39776.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADH1A / Plasmid: pKK2233 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / References: UniProt: P07327, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: 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: 2.3 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 6.5mg/ml enzyme, 3mM NAD+, 100mM Na-ACES, 13-15% PEG 6000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54059 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 1, 1999 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54059 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→30 Å / Num. all: 22908 / Num. obs: 22908 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 29.15 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.49→2.58 Å / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3 / Num. unique all: 2201 / % possible all: 78.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HSO Resolution: 2.49→30 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso mean: 29.15 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.49→30 Å
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Refine LS restraints |
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