+Open data
-Basic information
Entry | Database: PDB / ID: 1agn | ||||||
---|---|---|---|---|---|---|---|
Title | X-RAY STRUCTURE OF HUMAN SIGMA ALCOHOL DEHYDROGENASE | ||||||
Components | HUMAN SIGMA ALCOHOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information omega-hydroxydecanoate dehydrogenase / omega-hydroxydecanoate dehydrogenase activity / ethanol binding / aldehyde oxidase activity / all-trans-retinol dehydrogenase (NAD+) / fatty acid omega-oxidation / receptor antagonist activity / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity / : ...omega-hydroxydecanoate dehydrogenase / omega-hydroxydecanoate dehydrogenase activity / ethanol binding / aldehyde oxidase activity / all-trans-retinol dehydrogenase (NAD+) / fatty acid omega-oxidation / receptor antagonist activity / Ethanol oxidation / alcohol dehydrogenase (NAD+) activity / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / retinoid metabolic process / retinol binding / response to bacterium / response to ethanol / zinc ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | Hurley, T.D. / Xie, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1997 Title: X-ray structure of human class IV sigmasigma alcohol dehydrogenase. Structural basis for substrate specificity. Authors: Xie, P. / Parsons, S.H. / Speckhard, D.C. / Bosron, W.F. / Hurley, T.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1agn.cif.gz | 254.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1agn.ent.gz | 201.3 KB | Display | PDB format |
PDBx/mmJSON format | 1agn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1agn_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1agn_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1agn_validation.xml.gz | 54.1 KB | Display | |
Data in CIF | 1agn_validation.cif.gz | 73.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/1agn ftp://data.pdbj.org/pub/pdb/validation_reports/ag/1agn | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
2 |
| ||||||||||||||||
3 |
| ||||||||||||||||
4 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 39924.352 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: THE STRUCTURE CONTAINS ONE NAD+ PER SUBUNIT / Source: (gene. exp.) Homo sapiens (human) Description: PURCHASED FROM BOERINGER MANNHEIM (INDIANAPOLIS, IN) Gene: HUMAN SIGMA CDNA (ADH7) / Organ: STOMACH / Plasmid: PKK223-3 / Gene (production host): HUMAN SIGMA CDNA (ADH7) / Production host: Escherichia coli (E. coli) / References: UniProt: P40394, alcohol dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-NAD / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.5 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Wavelength: 1.5418 |
---|---|
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 22, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 34754 / % possible obs: 87 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.12 |
Reflection | *PLUS Highest resolution: 3 Å / Num. measured all: 79865 |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.5 Å / % possible obs: 83.5 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3→8 Å / σ(F): 1
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|