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- PDB-5ac0: ovis aries Aldehyde Dehydrogenase 1A1 in complex with a duocarmyc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ac0 | ||||||
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Title | ovis aries Aldehyde Dehydrogenase 1A1 in complex with a duocarmycin analog | ||||||
![]() | RETINAL DEHYDROGENASE 1 | ||||||
![]() | OXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE ACTIVITY / OXIDATION-REDUCTION PROCESS | ||||||
Function / homology | ![]() fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity ...fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / retinol metabolic process / retinoid metabolic process / NAD binding / axon / synapse / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Koch, M.F. / Harteis, S. / Blank, I.D. / Pestel, G. / Tietze, L.F. / Ochsenfeld, C. / Schneider, S. / Sieber, S.A. | ||||||
![]() | ![]() Title: Structural, Biochemical, and Computational Studies Reveal the Mechanism of Selective Aldehyde Dehydrogenase 1A1 Inhibition by Cytotoxic Duocarmycin Analogues. Authors: Koch, M.F. / Harteis, S. / Blank, I.D. / Pestel, G. / Tietze, L.F. / Ochsenfeld, C. / Schneider, S. / Sieber, S.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 220.6 KB | Display | ![]() |
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PDB format | ![]() | 175.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 43.7 KB | Display | |
Data in CIF | ![]() | 64.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5abmC ![]() 5ac1C ![]() 5ac2C ![]() 4x4lS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.7422, -0.6702, 0.001128), Vector: |
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Components
#1: Protein | Mass: 54885.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 31.9 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50.2 Å / Num. obs: 90805 / % possible obs: 99.8 % / Observed criterion σ(I): 10.56 / Redundancy: 6.8 % / Rmerge(I) obs: 0.12 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 6 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.43 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4X4L Resolution: 1.9→50.21 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.401 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.631 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50.21 Å
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Refine LS restraints |
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