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- PDB-7prm: CRYSTAL STRUCTURE OF HUMAN MONOGLYCERIDE LIPASE WITH COMPOUND 13 -

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Basic information

Entry
Database: PDB / ID: 7prm
TitleCRYSTAL STRUCTURE OF HUMAN MONOGLYCERIDE LIPASE WITH COMPOUND 13
ComponentsMonoglyceride lipase
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / SERINE ESTERASE
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 / 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 / triglyceride catabolic process / regulation of endocannabinoid signaling pathway / 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
: / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Lipases, serine active site. / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-81I / Monoglyceride lipase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGrether, U. / Gobbi, L. / Kuhn, B. / Collin, L. / Leibrock, L. / Heer, D. / Wittwer, M. / Benz, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Development of High Brain-Penetrant and Reversible Monoacylglycerol Lipase PET Tracers for Neuroimaging.
Authors: He, Y. / Schild, M. / Grether, U. / Benz, J. / Leibrock, L. / Heer, D. / Topp, A. / Collin, L. / Kuhn, B. / Wittwer, M. / Keller, C. / Gobbi, L.C. / Schibli, R. / Mu, L.
History
DepositionSep 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: 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
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0234
Polymers35,4661
Non-polymers5583
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint6 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.967, 127.448, 63.033
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-783-

HOH

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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-81I / (4~{R})-1-[4-(4-fluorophenyl)phenyl]-4-[4-(furan-2-ylcarbonyl)piperazin-1-yl]pyrrolidin-2-one


Mass: 433.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H24FN3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 51.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES 6.5 pH 6 %w/v PEG MME 5000 12 %v/v iso-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999883 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999883 Å / Relative weight: 1
ReflectionResolution: 1.65→73.5 Å / Num. obs: 43782 / % possible obs: 99.6 % / Redundancy: 6.77 % / CC1/2: 0.99 / Rsym value: 0.085 / Net I/σ(I): 8.47
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 6.88 % / Mean I/σ(I) obs: 0.62 / Num. unique obs: 6954 / CC1/2: 0.325 / Rsym value: 0.99 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house MAGL structure

Resolution: 1.65→73.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.963 / SU R Cruickshank DPI: 0.097 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.101 / SU Rfree Cruickshank DPI: 0.097
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 2134 -RANDOM
Rwork0.2064 ---
obs0.2079 43732 99.5 %-
Displacement parametersBiso mean: 46.48 Å2
Baniso -1Baniso -2Baniso -3
1--4.2106 Å20 Å20 Å2
2--3.9839 Å20 Å2
3---0.2268 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.65→73.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 0 40 312 2635
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082439HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.933329HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d855SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes422HARMONIC5
X-RAY DIFFRACTIONt_it2439HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion309SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2431SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion15.55
LS refinement shellResolution: 1.65→1.66 Å
RfactorNum. reflection% reflection
Rfree0.5022 45 -
Rwork0.4915 --
obs0.4921 875 99.54 %
Refinement TLS params.Origin x: 118.159 Å / Origin y: 21.1037 Å / Origin z: 0.0476 Å
111213212223313233
T0.3247 Å2-0.0156 Å2-0.0053 Å2--0.1471 Å2-0.0056 Å2---0.1383 Å2
L0.3245 °2-0.7734 °2-0.0124 °2-3.4212 °20.1922 °2--0.9209 °2
S-0.0266 Å °0.0836 Å °-0.0995 Å °0.0836 Å °0.04 Å °0.0759 Å °-0.0995 Å °0.0759 Å °-0.0134 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 295
2X-RAY DIFFRACTION1{ A|* }A301 - 303

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