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Yorodumi- PDB-5ac1: Sheep aldehyde dehydrogenase 1A1 with duocarmycin analog inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ac1 | ||||||
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Title | Sheep aldehyde dehydrogenase 1A1 with duocarmycin analog inhibitor | ||||||
Components | RETINAL DEHYDROGENASE 1 | ||||||
Keywords | OXIDOREDUCTASE / OXIDATION-REDUCTION PROCESS / ALDEHYDE DEHYDROGENASE ACTIVITY | ||||||
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: 2.08 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 | 5ac1.cif.gz | 406.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ac1.ent.gz | 332.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ac1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/5ac1 ftp://data.pdbj.org/pub/pdb/validation_reports/ac/5ac1 | HTTPS FTP |
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-Related structure data
Related structure data | 5abmC 5ac0C 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 7 - 500 / Label seq-ID: 8 - 501
NCS ensembles :
NCS oper: (Code: given Matrix: (0.8249, -0.000346, 0.5653), Vector: |
-Components
#1: Protein | Mass: 54885.590 Da / Num. of mol.: 4 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 | ChemComp-K9P / #3: Chemical | ChemComp-TXE / [[( #4: Chemical | ChemComp-MG / #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: 2.62 Å3/Da / Density % sol: 26.2 % / Description: NONE |
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Crystal grow | Temperature: 277 K Details: 100 MM BIS-TRIS, PH 6.0, 4.5-7% PEG5000, 150=225MM MGCL2, 4DEGREE |
-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: 2.1→49.4 Å / Num. obs: 134836 / % possible obs: 98.4 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.7 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4X4L Resolution: 2.08→49.38 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.556 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.202 / 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: 27.807 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→49.38 Å
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Refine LS restraints |
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