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Yorodumi- PDB-6try: Crystal structure of human Aldehyde dehydrogenase 1A3 in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6try | ||||||
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Title | Crystal structure of human Aldehyde dehydrogenase 1A3 in complex with MF13 inhibitor compound | ||||||
Components | Aldehyde dehydrogenase family 1 member A3 | ||||||
Keywords | OXIDOREDUCTASE / Dehydrogenase isoenzyme ALDH1A3 Selective Inhibitor High grade Glioma | ||||||
Function / homology | Function and homology information nucleus accumbens development / optic cup morphogenesis involved in camera-type eye development / olfactory pit development / Harderian gland development / retinoic acid biosynthetic process / embryonic eye morphogenesis / retinal dehydrogenase / embryonic camera-type eye development / aldehyde dehydrogenase [NAD(P)+] activity / RA biosynthesis pathway ...nucleus accumbens development / optic cup morphogenesis involved in camera-type eye development / olfactory pit development / Harderian gland development / retinoic acid biosynthetic process / embryonic eye morphogenesis / retinal dehydrogenase / embryonic camera-type eye development / aldehyde dehydrogenase [NAD(P)+] activity / RA biosynthesis pathway / righting reflex / retinal metabolic process / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / retinoic acid metabolic process / retinol metabolic process / inner ear morphogenesis / face development / thyroid hormone binding / neuromuscular process controlling balance / NAD+ binding / locomotory behavior / protein homotetramerization / positive regulation of apoptotic process / apoptotic process / protein homodimerization activity / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Gelardi, E.L.M. / Garavaglia, S. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2020 Title: Progress in the Field of Aldehyde Dehydrogenase Inhibitors: Novel Imidazo[1,2- a ]pyridines against the 1A Family. Authors: Quattrini, L. / Gelardi, E.L.M. / Petrarolo, G. / Colombo, G. / Ferraris, D.M. / Picarazzi, F. / Rizzi, M. / Garavaglia, S. / La Motta, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6try.cif.gz | 198.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6try.ent.gz | 157.8 KB | Display | PDB format |
PDBx/mmJSON format | 6try.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/6try ftp://data.pdbj.org/pub/pdb/validation_reports/tr/6try | HTTPS FTP |
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-Related structure data
Related structure data | 5fhzS 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: 56177.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1A3, ALDH6 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P47895, retinal dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.57 Å3/Da / Density % sol: 52.12 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / Details: 0.4 M sodium malonate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9677 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→47.96 Å / Num. obs: 48135 / % possible obs: 98.8 % / Redundancy: 4.6 % / Rpim(I) all: 0.061 / Rrim(I) all: 0.132 / Rsym value: 0.117 / Net I/av σ(I): 5.5 / Net I/σ(I): 10.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FHZ Resolution: 2.9→47.96 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0.24 / Phase error: 27.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.42 Å2 / Biso mean: 61.173 Å2 / Biso min: 21.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→47.96 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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