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Yorodumi- PDB-5ac0: ovis aries Aldehyde Dehydrogenase 1A1 in complex with a duocarmyc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ac0 | ||||||
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Title | ovis aries Aldehyde Dehydrogenase 1A1 in complex with a duocarmycin analog | ||||||
Components | RETINAL DEHYDROGENASE 1 | ||||||
Keywords | OXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE ACTIVITY / OXIDATION-REDUCTION PROCESS | ||||||
Function / homology | Function and homology information fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase activity / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / 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 / aminobutyraldehyde dehydrogenase activity / retinal dehydrogenase / aminobutyraldehyde dehydrogenase / 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 | OVIS ARIES (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Koch, M.F. / Harteis, S. / Blank, I.D. / Pestel, G. / Tietze, L.F. / Ochsenfeld, C. / Schneider, S. / Sieber, S.A. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ac0.cif.gz | 220.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ac0.ent.gz | 175.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ac0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/5ac0 ftp://data.pdbj.org/pub/pdb/validation_reports/ac/5ac0 | HTTPS FTP |
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-Related structure data
Related structure data | 5abmC 5ac1C 5ac2C 4x4lS C: citing same article (ref.) 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.7422, -0.6702, 0.001128), Vector: |
-Components
#1: Protein | Mass: 54885.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) OVIS ARIES (sheep) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51977, retinal dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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