+Open data
-Basic information
Entry | Database: PDB / ID: 7qk9 | ||||||
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Title | Crystal structure of the ALDH1A3-ATP complex | ||||||
Components | Aldehyde dehydrogenase family 1 member A3 | ||||||
Keywords | OXIDOREDUCTASE / ALDH1A3 / Aldehyde dehydrogenase family 1 member A3 / ATP | ||||||
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 / thyroid hormone binding / face development / 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: 1.782 Å | ||||||
Authors | Castellvi, A. / Farres, J. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Commun Biol / Year: 2022 Title: Structural and biochemical evidence that ATP inhibits the cancer biomarker human aldehyde dehydrogenase 1A3. Authors: Castellvi, A. / Pequerul, R. / Barracco, V. / Juanhuix, J. / Pares, X. / Farres, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qk9.cif.gz | 216.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qk9.ent.gz | 167.3 KB | Display | PDB format |
PDBx/mmJSON format | 7qk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/7qk9 ftp://data.pdbj.org/pub/pdb/validation_reports/qk/7qk9 | HTTPS FTP |
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-Related structure data
Related structure data | 7qk7C 7qk8C 5fhzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 53813.703 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 (E. coli) / References: UniProt: P47895, retinal dehydrogenase |
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-Non-polymers , 6 types, 623 molecules
#2: Chemical | #3: Chemical | ChemComp-PEG / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.72 Å3/Da / Density % sol: 54.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: The crystallization solution consisted of 100 mM BIS-Tris, pH 5.5, 2-2.2 M ammonium sulfate and 5% PEG 400. |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→48.19 Å / Num. obs: 111992 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 36.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.78→1.81 Å / Rmerge(I) obs: 2.369 / Num. unique obs: 4978 / CC1/2: 0.57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5fhz Resolution: 1.782→48.19 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.114 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.104
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Displacement parameters | Biso mean: 45.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.782→48.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.782→1.8 Å
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