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- PDB-8rvf: CRYSTAL STRUCTURE OF HUMAN MONOGLYCERIDE LIPASE IN COMPLEX WITH C... -

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Basic information

Entry
Database: PDB / ID: 8rvf
TitleCRYSTAL STRUCTURE OF HUMAN MONOGLYCERIDE LIPASE IN COMPLEX WITH COMPOUND 5
ComponentsMonoglyceride lipase
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / 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 / lysophospholipase 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: 1.43 Å
AuthorsLeibrock, L. / Hentsch, A. / Nazare, M. / Grether, U. / Kuhn, B. / Blaising, J. / Benz, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Highly Specific Miniaturized Fluorescent Monoacylglycerol Lipase Probes Enable Translational Research.
Authors: Hentsch, A. / Guberman, M. / Radetzki, S. / Kaushik, S. / Huizenga, M. / He, Y. / Contzen, J. / Kuhn, B. / Benz, J. / Schippers, M. / Paul, J. / Leibrock, L. / Collin, L. / Wittwer, M. / ...Authors: Hentsch, A. / Guberman, M. / Radetzki, S. / Kaushik, S. / Huizenga, M. / He, Y. / Contzen, J. / Kuhn, B. / Benz, J. / Schippers, M. / Paul, J. / Leibrock, L. / Collin, L. / Wittwer, M. / Topp, A. / O'Hara, F. / Heer, D. / Hochstrasser, R. / Blaising, J. / von Kries, J.P. / Mu, L. / van der Stelt, M. / Mergenthaler, P. / Lipstein, N. / Grether, U. / Nazare, M.
History
DepositionFeb 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)36,1835
Polymers35,4661
Non-polymers7184
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.446, 127.312, 62.845
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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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-A1H35 / [6-[[2,2-bis(fluoranyl)-1$l^{4},3-diaza-2$l^{4}-boratricyclo[7.3.0.0^{3,7}]dodeca-1(12),4,6,8,10-pentaen-8-yl]methyl]-2-azaspiro[3.3]heptan-2-yl]-[6-(3-cyclopropyl-1,2,4-triazol-1-yl)-2-azaspiro[3.3]heptan-2-yl]methanone


Mass: 531.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H32BF2N7O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6.5, 11% PEG MME5K, 12% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Dec 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→20.18 Å / Num. obs: 67210 / % possible obs: 100 % / Redundancy: 7.47 % / CC1/2: 0.99 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.34
Reflection shellResolution: 1.43→1.53 Å / Rmerge(I) obs: 1 / Num. unique obs: 12202 / CC1/2: 0.661

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→63.66 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU R Cruickshank DPI: 0.06 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.063 / SU Rfree Blow DPI: 0.066 / SU Rfree Cruickshank DPI: 0.063
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3354 -RANDOM
Rwork0.1935 ---
obs0.1948 67130 99.9 %-
Displacement parametersBiso mean: 36.25 Å2
Baniso -1Baniso -2Baniso -3
1--5.9126 Å20 Å20 Å2
2--4.1436 Å20 Å2
3---1.7691 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.43→63.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 51 307 2602
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112448HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.073358HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d869SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes445HARMONIC5
X-RAY DIFFRACTIONt_it2448HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion308SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2501SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.66
X-RAY DIFFRACTIONt_other_torsion15.85
LS refinement shellResolution: 1.43→1.44 Å
RfactorNum. reflection% reflection
Rfree0.466 74 -
Rwork0.4831 --
obs0.4822 1343 99.85 %
Refinement TLS params.Origin x: 118.849 Å / Origin y: 20.4231 Å / Origin z: -0.0518 Å
111213212223313233
T0.1273 Å20.0068 Å2-0.0047 Å2--0.0813 Å2-0.0008 Å2---0.0493 Å2
L0 °2-0.2754 °20.0141 °2-1.6555 °2-0.0423 °2--0.2839 °2
S-0.0324 Å °0.079 Å °-0.017 Å °0.079 Å °0.0054 Å °-0.0117 Å °-0.017 Å °-0.0117 Å °0.0271 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A6 - 295
2X-RAY DIFFRACTION1{ A|* }A301

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