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Yorodumi- PDB-3jwe: Crystal structure of human mono-glyceride lipase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jwe | ||||||
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Title | Crystal structure of human mono-glyceride lipase in complex with SAR629 | ||||||
Components | MGLL protein | ||||||
Keywords | HYDROLASE / alpha-beta hydrolase | ||||||
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 / triglyceride catabolic process / regulation of endocannabinoid signaling pathway / monoacylglycerol lipase activity / regulation of sensory perception of pain / lysophospholipase activity ...Arachidonate production from DAG / acylglycerol catabolic process / Acyl chain remodeling of DAG and TAG / acylglycerol lipase / monoacylglycerol catabolic process / triglyceride catabolic process / regulation of endocannabinoid signaling pathway / monoacylglycerol lipase activity / regulation of sensory perception of pain / lysophospholipase activity / Triglyceride catabolism / regulation of signal transduction / arachidonate metabolic process / 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: 2.7 Å | ||||||
Authors | Bertrand, T. / Auge, F. / Houtmann, J. / Rak, A. / Vallee, F. / Mikol, V. / Berne, P.F. / Michot, N. / Cheuret, D. / Hoornaert, C. / Mathieu, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structural basis for human monoglyceride lipase inhibition. Authors: Bertrand, T. / Auge, F. / Houtmann, J. / Rak, A. / Vallee, F. / Mikol, V. / Berne, P.F. / Michot, N. / Cheuret, D. / Hoornaert, C. / Mathieu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jwe.cif.gz | 120.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jwe.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 3jwe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jwe_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3jwe_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3jwe_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 3jwe_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/3jwe ftp://data.pdbj.org/pub/pdb/validation_reports/jw/3jwe | HTTPS FTP |
-Related structure data
Related structure data | 3jw8SC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35292.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MGLL, hCG_40840 / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q6IBG9, UniProt: Q99685*PLUS, acylglycerol lipase #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | F4P 315 B IS AN UNCLEAVED FORM OF THE MOLECULE. F4P 314 A AND B IS THE RESULT OF THE CATALYTIC ...F4P 315 B IS AN UNCLEAVED FORM OF THE MOLECULE. F4P 314 A AND B IS THE RESULT OF THE CATALYTIC REACTION OCCURING IN THE CRYSTAL. | |
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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: 2.74 Å3/Da / Density % sol: 55.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50mM MES, 40% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2008 |
Radiation | Monochromator: Diamonds 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→63.7 Å / Num. all: 18831 / Num. obs: 18831 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 52.05 Å2 / Rsym value: 0.104 |
Reflection shell | Resolution: 2.7→2.86 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.356 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3JW8 Resolution: 2.7→63.63 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 39.08 Å2
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Refine analyze | Luzzati coordinate error obs: 0.337 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→63.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.86 Å / Total num. of bins used: 9
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