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Yorodumi- PDB-5syn: Cocrystal structure of the human acyl protein thioesterase 2 with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5syn | |||||||||
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Title | Cocrystal structure of the human acyl protein thioesterase 2 with an isoform-selective inhibitor, ML349 | |||||||||
Components | Acyl-protein thioesterase 2 | |||||||||
Keywords | hydrolase/hydrolase inhibitor / hydrolase / inhibitor / thioesterase / hydrolase-hydrolase inhibitor complex | |||||||||
Function / homology | Function and homology information prostaglandin catabolic process / protein depalmitoylation / palmitoyl[protein] hydrolase / acylglycerol catabolic process / palmitoyl-(protein) hydrolase activity / L1CAM interactions / lysophospholipase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / Golgi stack / carboxylic ester hydrolase activity ...prostaglandin catabolic process / protein depalmitoylation / palmitoyl[protein] hydrolase / acylglycerol catabolic process / palmitoyl-(protein) hydrolase activity / L1CAM interactions / lysophospholipase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / Golgi stack / carboxylic ester hydrolase activity / fatty acid metabolic process / axon guidance / cadherin binding / extracellular exosome / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | |||||||||
Authors | Stuckey, J.A. / Labby, K.J. / Meagher, J.L. / Won, S.J. / Martin, B.R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: ACS Chem. Biol. / Year: 2016 Title: Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2). Authors: Won, S.J. / Davda, D. / Labby, K.J. / Hwang, S.Y. / Pricer, R. / Majmudar, J.D. / Armacost, K.A. / Rodriguez, L.A. / Rodriguez, C.L. / Chong, F.S. / Torossian, K.A. / Palakurthi, J. / Hur, E. ...Authors: Won, S.J. / Davda, D. / Labby, K.J. / Hwang, S.Y. / Pricer, R. / Majmudar, J.D. / Armacost, K.A. / Rodriguez, L.A. / Rodriguez, C.L. / Chong, F.S. / Torossian, K.A. / Palakurthi, J. / Hur, E.S. / Meagher, J.L. / Brooks, C.L. / Stuckey, J.A. / Martin, B.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5syn.cif.gz | 344.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5syn.ent.gz | 282.8 KB | Display | PDB format |
PDBx/mmJSON format | 5syn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/5syn ftp://data.pdbj.org/pub/pdb/validation_reports/sy/5syn | HTTPS FTP |
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-Related structure data
Related structure data | 5symC 1fj2S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 24764.959 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LYPLA2, APT2 / Production host: Escherichia coli (E. coli) References: UniProt: O95372, Hydrolases; Acting on ester bonds; Thioester hydrolases #2: Chemical | ChemComp-71T / #3: Chemical | ChemComp-EDO / #4: 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: 2.18 Å3/Da / Density % sol: 43.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 mM sodium citrate pH 5.5, 20-24% PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→55.81 Å / Num. obs: 97049 / % possible obs: 93.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB:1FJ2 Chain A Resolution: 1.64→55.81 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 22.553 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→55.81 Å
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