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Yorodumi- PDB-3szb: Crystal structure of human ALDH3A1 modified with the beta-elimina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3szb | ||||||
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Title | Crystal structure of human ALDH3A1 modified with the beta-elimination product of Aldi-1; 1-phenyl- 2-propen-1-one | ||||||
Components | Aldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / ALDH / Aldi-1 / inhibitor / Rossmann Fold / Covalent Adduct / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information aldehyde dehydrogenase [NAD(P)+] / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / aldehyde dehydrogenase [NAD(P)+] activity / cellular aldehyde metabolic process / aldehyde dehydrogenase (NAD+) activity / Phase I - Functionalization of compounds / xenobiotic metabolic process / lipid metabolic process ...aldehyde dehydrogenase [NAD(P)+] / 3-chloroallyl aldehyde dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / aldehyde dehydrogenase [NAD(P)+] activity / cellular aldehyde metabolic process / aldehyde dehydrogenase (NAD+) activity / Phase I - Functionalization of compounds / xenobiotic metabolic process / lipid metabolic process / endoplasmic reticulum / extracellular space / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Khanna, M. / Hurley, T.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Discovery of a novel class of covalent inhibitor for aldehyde dehydrogenases. Authors: Khanna, M. / Chen, C.H. / Kimble-Hill, A. / Parajuli, B. / Perez-Miller, S. / Baskaran, S. / Kim, J. / Dria, K. / Vasiliou, V. / Mochly-Rosen, D. / Hurley, T.D. #1: Journal: BIOCHEM.PHARM. / Year: 2008 Title: A point mutation produced a class 3 aldehyde dehydrogenase with increased protective ability against the killing effect of cyclophosphamide Authors: Ho, K.K. / Mukhopadhyay, A. / Li, Y.F. / Mukhopadhyay, S. / Weiner, H. #2: Journal: Nat.Struct.Mol.Biol. / Year: 1997 Title: The first structure of an aldehyde dehydrogenase reveals novel interactions between NAD and the Rossmann Fold Authors: Liu, Z.J. / Sun, Y.J. / Rose, J. / Chung, Y.J. / Hsiao, C.D. / Chang, W.R. / Kuo, I. / Perozich, J. / Lindahl, R. / Hempel, J. / Wang, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3szb.cif.gz | 218.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3szb.ent.gz | 171.5 KB | Display | PDB format |
PDBx/mmJSON format | 3szb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/3szb ftp://data.pdbj.org/pub/pdb/validation_reports/sz/3szb | HTTPS FTP |
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-Related structure data
Related structure data | 3sz9C 3szaC 1ad3S 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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-Components
#1: Protein | Mass: 52245.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH3A1, ALDH3 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P30838, aldehyde dehydrogenase [NAD(P)+] #2: Chemical | ChemComp-K / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | THE STARTING MATERIAL IS 1-PHENYL-2-PROPEN-1-ONE. IT BINDS COVALENTLY TO CYS 243. I1E CORRESPONDS ...THE STARTING MATERIAL IS 1-PHENYL-2-PROPEN-1-ONE. IT BINDS COVALENTLY | |
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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: 2.13 Å3/Da / Density % sol: 42.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: 0.2 M potassium acetate, 18% PEG 3350, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9869 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9869 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.51→50 Å / Num. obs: 137498 / % possible obs: 97.7 % / Observed criterion σ(I): 0.2 / Redundancy: 4.4 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.058 / Χ2: 1.037 / Net I/σ(I): 13.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AD3 Resolution: 1.51→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.2245 / WRfactor Rwork: 0.1997 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8785 / SU B: 1.304 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0816 / SU Rfree: 0.0795 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.079 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.27 Å2 / Biso mean: 20.6178 Å2 / Biso min: 8.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.549 Å / Total num. of bins used: 20
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