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- PDB-9g4m: Crystal structure of monoacylglycerol lipase with BODIPY labeled probe -

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Basic information

Entry
Database: PDB / ID: 9g4m
TitleCrystal structure of monoacylglycerol lipase with BODIPY labeled probe
ComponentsMonoglyceride lipase
KeywordsHYDROLASE / Serine Esterase
Function / homology
Function and homology information


Arachidonate production from DAG / Acyl chain remodeling of DAG and TAG / acylglycerol lipase / acylglycerol catabolic process / 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 / Acyl chain remodeling of DAG and TAG / acylglycerol lipase / acylglycerol catabolic process / monoacylglycerol catabolic process / regulation of endocannabinoid signaling pathway / triglyceride catabolic process / monoacylglycerol lipase activity / arachidonate metabolic process / regulation of sensory perception of pain / phosphatidylcholine lysophospholipase activity / carboxylic ester hydrolase activity / Triglyceride catabolism / regulation of signal transduction / lipid metabolic process / fatty acid biosynthetic process / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / regulation of inflammatory response / inflammatory response / endoplasmic reticulum membrane / protein homodimerization activity / membrane / plasma membrane / cytosol
Similarity search - Function
: / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Lipases, serine active site. / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / Monoglyceride lipase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsGuberman, M. / Hentsch, A. / Radetzki, S. / Kaushik, S. / Huizenga, M. / van der Stelt, M. / Paul, J. / Schippers, M. / Hochstrasser, R. / von Kries, J.P. ...Guberman, M. / Hentsch, A. / Radetzki, S. / Kaushik, S. / Huizenga, M. / van der Stelt, M. / Paul, J. / Schippers, M. / Hochstrasser, R. / von Kries, J.P. / Blaising, J. / Lipstein, N. / Nazare, M. / Grether, U. / Kuhn, B. / Walter, A. / Benz, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: A Highly Selective and Versatile Probe Platform for Visualization of Monoacylglycerol Lipase.
Authors: Hentsch, A. / Guberman, M. / Radetzki, S. / Kaushik, S. / Huizenga, M. / Paul, J. / Schippers, M. / Benz, J. / Kuhn, B. / Heer, D. / Topp, A. / Esteves Gloria, L. / Walter, A. / ...Authors: Hentsch, A. / Guberman, M. / Radetzki, S. / Kaushik, S. / Huizenga, M. / Paul, J. / Schippers, M. / Benz, J. / Kuhn, B. / Heer, D. / Topp, A. / Esteves Gloria, L. / Walter, A. / Hochstrasser, R. / Wittwer, M.B. / von Kries, J.P. / Collin, L. / Blaising, J. / van der Stelt, M. / Lipstein, N. / Grether, U. / Nazare, M.
History
DepositionJul 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,63710
Polymers35,4661
Non-polymers1,1719
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint22 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.896, 127.245, 62.206
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Monoglyceride lipase / MGL / HU-K5 / Lysophospholipase homolog / Lysophospholipase-like / Monoacylglycerol lipase / MAGL


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
#2: Chemical ChemComp-A1IIH / 3-[2,2-bis(fluoranyl)-10,12-dimethyl-1$l^{4},3-diaza-2$l^{4}-boratricyclo[7.3.0.0^{3,7}]dodeca-1(12),4,6,8,10-pentaen-4-yl]-~{N}-[2-[2-[[2-[(6-oxidanylidene-7-oxa-2,5-diazaspiro[3.4]octan-2-yl)carbonyl]-2-azaspiro[3.3]heptan-6-yl]methyl]phenoxy]ethyl]propanamide


Mass: 674.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H41BF2N6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8 %v/v 1-Propan 0.1 M MES pH 6.5 12 %w/v PEG MME 5K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885603 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885603 Å / Relative weight: 1
ReflectionResolution: 1.41→72.87 Å / Num. obs: 68084 / % possible obs: 99.9 % / Redundancy: 10.36 % / Biso Wilson estimate: 18.94 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.97
Reflection shellResolution: 1.41→1.5 Å / Rmerge(I) obs: 0.99 / Num. unique obs: 11347 / CC1/2: 0.552

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286+SVNrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→36.16 Å / SU ML: 0.1793 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.7821
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1846 3323 4.89 %
Rwork0.1573 64574 -
obs0.1586 67897 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.38 Å2
Refinement stepCycle: LAST / Resolution: 1.41→36.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 81 210 2535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542453
X-RAY DIFFRACTIONf_angle_d0.83783348
X-RAY DIFFRACTIONf_chiral_restr0.0765376
X-RAY DIFFRACTIONf_plane_restr0.007452
X-RAY DIFFRACTIONf_dihedral_angle_d13.8513950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.430.36471430.36842609X-RAY DIFFRACTION98.64
1.43-1.450.39991230.34212663X-RAY DIFFRACTION99.11
1.45-1.470.39091330.32642632X-RAY DIFFRACTION98.89
1.47-1.50.29011300.29972679X-RAY DIFFRACTION99.19
1.5-1.520.3081370.27992654X-RAY DIFFRACTION99.22
1.52-1.550.29351280.26122672X-RAY DIFFRACTION99.47
1.55-1.580.2641300.24432668X-RAY DIFFRACTION99.43
1.58-1.610.26861490.22692629X-RAY DIFFRACTION99.43
1.61-1.650.28091250.22352706X-RAY DIFFRACTION99.86
1.65-1.690.27281480.212678X-RAY DIFFRACTION99.68
1.69-1.730.21861470.18762648X-RAY DIFFRACTION99.79
1.73-1.780.19351440.16212675X-RAY DIFFRACTION99.68
1.78-1.830.19521360.15282660X-RAY DIFFRACTION99.89
1.83-1.890.19971310.14132727X-RAY DIFFRACTION99.9
1.89-1.960.18241440.1352657X-RAY DIFFRACTION99.57
1.96-2.030.16761460.12812687X-RAY DIFFRACTION99.93
2.03-2.130.1421300.11942700X-RAY DIFFRACTION99.82
2.13-2.240.15241460.12272674X-RAY DIFFRACTION99.89
2.24-2.380.16311450.12422716X-RAY DIFFRACTION99.83
2.38-2.560.15261600.13532690X-RAY DIFFRACTION100
2.56-2.820.16631390.13462734X-RAY DIFFRACTION99.97
2.82-3.230.17071370.14122755X-RAY DIFFRACTION100
3.23-4.070.1571320.13882773X-RAY DIFFRACTION99.86
4.07-36.160.17281400.16282888X-RAY DIFFRACTION99.9

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