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Yorodumi- PDB-4h80: Crystal structure of human ALDH3A1 with its isozyme selective inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h80 | ||||||
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Title | Crystal structure of human ALDH3A1 with its isozyme selective inhibitor - N-[4-(4-methylsulfonyl-2-nitroanilino)phenyl]acetamide | ||||||
Components | Aldehyde dehydrogenase, dimeric NADP-preferring | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Catalyzes benzaldehyde / Rossmann fold / Dehydrogenase / NADP+ binding / 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: 2.5 Å | ||||||
Authors | Hurley, T.D. / Parajuli, B. | ||||||
Citation | Journal: To be Published Title: Kinetic and Structural Characterization of a Selective Inhibitor for Human ALDH3A1 Authors: Parajuli, B. / Georgiadis, T. / Fishel, M.L. / Hurley, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h80.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4h80.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 4h80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/4h80 ftp://data.pdbj.org/pub/pdb/validation_reports/h8/4h80 | HTTPS FTP |
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-Related structure data
Related structure data | 3szaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 5 - 432 / Label seq-ID: 22 - 449
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-Components
#1: Protein | Mass: 52245.738 Da / Num. of mol.: 8 / Mutation: S133A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH3, ALDH3A1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) References: UniProt: P30838, aldehyde dehydrogenase [NAD(P)+] #2: Chemical | ChemComp-04T / #3: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44.15 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Potassium acetate, 20 % PEG 3350, (3 microliters of 3 mg/mL of ALDH3A1 + 3 microlitres of mother liquor), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9869 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2010 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9869 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 123251 / Num. obs: 115363 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.2 / Redundancy: 2.2 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.25 / Rsym value: 0.067 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4489 / % possible all: 72.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SZA Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.915 / SU B: 32.465 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 62.888 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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