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Yorodumi- PDB-6dy2: Guinea pig N-acylethanolamine-hydrolyzing acid amidase (NAAA) cov... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dy2 | ||||||
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Title | Guinea pig N-acylethanolamine-hydrolyzing acid amidase (NAAA) covalently bound to beta-lactam inhibitor ARN726 | ||||||
Components | (N-acylethanolamine acid amidase ...) x 2 | ||||||
Keywords | HYDROLASE / endocannabinoid / lipase | ||||||
Function / homology | Function and homology information N-(long-chain-acyl)ethanolamine deacylase / sphingosine metabolic process / N-(long-chain-acyl)ethanolamine deacylase activity / ceramidase / N-acylsphingosine amidohydrolase activity / : / N-acylethanolamine metabolic process / N-acylphosphatidylethanolamine metabolic process / fatty acid amide hydrolase activity / lipid catabolic process ...N-(long-chain-acyl)ethanolamine deacylase / sphingosine metabolic process / N-(long-chain-acyl)ethanolamine deacylase activity / ceramidase / N-acylsphingosine amidohydrolase activity / : / N-acylethanolamine metabolic process / N-acylphosphatidylethanolamine metabolic process / fatty acid amide hydrolase activity / lipid catabolic process / fatty acid metabolic process / lysosome / membrane Similarity search - Function | ||||||
Biological species | Cavia porcellus (domestic guinea pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.706 Å | ||||||
Authors | Gorelik, A. / Gebai, A. / Illes, K. / Piomelli, D. / Nagar, B. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Molecular mechanism of activation of the immunoregulatory amidase NAAA. Authors: Gorelik, A. / Gebai, A. / Illes, K. / Piomelli, D. / Nagar, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dy2.cif.gz | 259.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dy2.ent.gz | 210.6 KB | Display | PDB format |
PDBx/mmJSON format | 6dy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/6dy2 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/6dy2 | HTTPS FTP |
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-Related structure data
Related structure data | 6dxwC 6dxxC 6dxyC 6dxzC 6dy0C 6dy1C 6dy3C 5u7zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-N-acylethanolamine acid amidase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 11686.366 Da / Num. of mol.: 2 / Fragment: residues 21-115 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: NAAA / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: H0VCJ6, N-(long-chain-acyl)ethanolamine deacylase #2: Protein | Mass: 25967.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: NAAA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: H0VCJ6 |
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-Sugars , 1 types, 6 molecules
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 148 molecules
#4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | #7: 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: 2.78 Å3/Da / Density % sol: 55.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.2 M KH2PO4 and 20 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.706→50 Å / Num. obs: 23122 / % possible obs: 98 % / Redundancy: 11.6 % / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.706→2.8 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U7Z Resolution: 2.706→49.431 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.706→49.431 Å
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Refine LS restraints |
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LS refinement shell |
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