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Yorodumi- PDB-8aqf: CRYSTAL STRUCTURE OF HUMAN MONOGLYCERIDE LIPASE WITH COMPOUND LEI-515 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aqf | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN MONOGLYCERIDE LIPASE WITH COMPOUND LEI-515 | ||||||
Components | Monoglyceride lipase | ||||||
Keywords | HYDROLASE / Monoacylglycerol lipase / MAGL / inhibitor | ||||||
Function / homology | Function and homology information Arachidonate production from DAG / acylglycerol catabolic process / Acyl chain remodeling of DAG and TAG / acylglycerol lipase / monoacylglycerol catabolic process / regulation of endocannabinoid signaling pathway / triglyceride catabolic process / monoacylglycerol lipase activity / arachidonate metabolic process / regulation of sensory perception of pain ...Arachidonate production from DAG / acylglycerol catabolic process / Acyl chain remodeling of DAG and TAG / acylglycerol lipase / monoacylglycerol catabolic process / regulation of endocannabinoid signaling pathway / triglyceride catabolic process / monoacylglycerol lipase activity / arachidonate metabolic process / regulation of sensory perception of pain / lysophospholipase activity / Triglyceride catabolism / regulation of signal transduction / lipid metabolic process / fatty acid biosynthetic process / regulation of inflammatory response / inflammatory response / endoplasmic reticulum membrane / protein homodimerization activity / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Jiang, M. / Huizenga, M. / Wirt, J. / Paloczi, J. / Amedi, A. / van der Berg, R. / Benz, J. / Collin, L. / Deng, H. / Driever, W. ...Jiang, M. / Huizenga, M. / Wirt, J. / Paloczi, J. / Amedi, A. / van der Berg, R. / Benz, J. / Collin, L. / Deng, H. / Driever, W. / Florea, B. / Grether, U. / Janssen, A. / Heitman, L. / Lam, T.W. / Mohr, F. / Pavlovic, A. / Ruf, I. / Rutjes, H. / Stevens, F. / van der Vliet, D. / van der Wel, T. / Wittwer, M. / Boeckel, C. / Pacher, P. / Hohmann, A. / van der Stelt, M. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Discovery of a peripheral restricted, reversible monoacylglycerol lipase inhibitor that reduces liver injury and chemotherapy-induced neuropathy Authors: Jiang, M. / van der Stelt, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aqf.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aqf.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 8aqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aqf_validation.pdf.gz | 710 KB | Display | wwPDB validaton report |
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Full document | 8aqf_full_validation.pdf.gz | 711.4 KB | Display | |
Data in XML | 8aqf_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 8aqf_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/8aqf ftp://data.pdbj.org/pub/pdb/validation_reports/aq/8aqf | HTTPS FTP |
-Related structure data
Related structure data | 3pe6S S: Starting model for refinement |
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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
#1: Protein | Mass: 35465.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MGLL / Production host: Escherichia coli (E. coli) / References: UniProt: Q99685, acylglycerol lipase |
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#2: Chemical | ChemComp-NUX / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M MES pH 6.5, 6 to 13% PEG MME5K, 12% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00009 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00009 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→45.81 Å / Num. obs: 51415 / % possible obs: 99.6 % / Redundancy: 6.62 % / CC1/2: 0.9985 / Rsym value: 0.0631 / Net I/σ(I): 11.69 |
Reflection shell | Resolution: 1.55→1.65 Å / Num. unique obs: 8639 / CC1/2: 0.5966 / Rsym value: 0.7885 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PE6 Resolution: 1.55→45.81 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 3.972 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.064 / ESU R Free: 0.065 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.073 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→45.81 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 120.3284 Å / Origin y: 19.9573 Å / Origin z: -0.7198 Å
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Refinement TLS group | Selection: ALL |