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- PDB-9i5j: CRYSTAL STRUCTURE OF HUMAN MONOACYLGLYCEROL LIPASE WITH COMPOUND 27 -

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Basic information

Entry
Database: PDB / ID: 9i5j
TitleCRYSTAL STRUCTURE OF HUMAN MONOACYLGLYCEROL LIPASE WITH COMPOUND 27
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 catabolic process / 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 / Acyl chain remodeling of DAG and TAG / acylglycerol catabolic process / 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 / phosphatidylcholine lysophospholipase A1 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: 1.48 Å
AuthorsWalter, A. / Atz, K. / Stenzhorn, Y. / Nippa, D. / Grether, U. / Kuhn, B. / Martin, R. / Benz, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Nat Commun / Year: 2025
Title: Expediting hit-to-lead progression in drug discovery through reaction prediction and multi-dimensional optimization.
Authors: Nippa, D.F. / Atz, K. / Stenzhorn, Y. / Muller, A.T. / Tosstorff, A. / Benz, J. / Binch, H. / Burkler, M. / Haider, A. / Heer, D. / Hochstrasser, R. / Kramer, C. / Reutlinger, M. / ...Authors: Nippa, D.F. / Atz, K. / Stenzhorn, Y. / Muller, A.T. / Tosstorff, A. / Benz, J. / Binch, H. / Burkler, M. / Haider, A. / Heer, D. / Hochstrasser, R. / Kramer, C. / Reutlinger, M. / Schneider, P. / Shema, T. / Topp, A. / Walter, A. / Wittwer, M.B. / Wolfard, J. / Kuhn, B. / van der Stelt, M. / Martin, R.E. / Grether, U. / Schneider, G.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJan 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2026Group: 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

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Assembly

Deposited unit
A: Monoglyceride lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0833
Polymers35,4661
Non-polymers6172
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-1 kcal/mol
Surface area12230 Å2
Unit cell
Length a, b, c (Å)89.179, 127.121, 62.526
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-A1IZ4 / [4-(5-chloranyl-[1,3]oxazolo[4,5-b]pyridin-2-yl)piperazin-1-yl]-[2-[4-(1-cyclobutylcyclopropyl)pyridin-3-yl]-1,3-benzoxazol-6-yl]methanone


Mass: 555.027 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H27ClN6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 10% PEG MME5K, 12% isopropanol

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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 EIGER2 S 16M / Detector: PIXEL / Date: May 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885603 Å / Relative weight: 1
ReflectionResolution: 1.48→44.57 Å / Num. obs: 59049 / % possible obs: 99.2 % / Redundancy: 10.06 % / Biso Wilson estimate: 22.45 Å2 / CC1/2: 0.998 / Rsym value: 0.09 / Net I/σ(I): 9.09
Reflection shellResolution: 1.48→1.58 Å / Num. unique obs: 10344 / CC1/2: 0.535 / Rsym value: 0.97

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→38.27 Å / SU ML: 0.2231 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.3557
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2057 2903 4.94 %
Rwork0.1882 55909 -
obs0.1891 58812 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.17 Å2
Refinement stepCycle: LAST / Resolution: 1.48→38.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 44 222 2510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752411
X-RAY DIFFRACTIONf_angle_d0.93773300
X-RAY DIFFRACTIONf_chiral_restr0.0801372
X-RAY DIFFRACTIONf_plane_restr0.0089422
X-RAY DIFFRACTIONf_dihedral_angle_d12.8536930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.50511480.45832578X-RAY DIFFRACTION97.39
1.5-1.530.46111270.44462594X-RAY DIFFRACTION96.83
1.53-1.560.43881280.41552632X-RAY DIFFRACTION97.87
1.56-1.590.44681310.39152592X-RAY DIFFRACTION97.84
1.59-1.620.31651450.35462579X-RAY DIFFRACTION97.6
1.62-1.660.3711300.3382634X-RAY DIFFRACTION98.33
1.66-1.690.34981280.31352639X-RAY DIFFRACTION98.4
1.69-1.740.30061210.28822638X-RAY DIFFRACTION98.64
1.74-1.780.25021210.26412680X-RAY DIFFRACTION98.7
1.78-1.840.2921250.22852632X-RAY DIFFRACTION99.07
1.84-1.90.24331710.21642643X-RAY DIFFRACTION99.12
1.9-1.960.25131260.19852647X-RAY DIFFRACTION99.07
1.96-2.040.22051630.18542654X-RAY DIFFRACTION99.51
2.04-2.130.1991360.17352657X-RAY DIFFRACTION99.15
2.13-2.250.17751510.16812653X-RAY DIFFRACTION99.54
2.25-2.390.22461460.17512691X-RAY DIFFRACTION99.54
2.39-2.570.22361200.16612713X-RAY DIFFRACTION99.86
2.57-2.830.17571440.17212711X-RAY DIFFRACTION99.69
2.83-3.240.17141490.17212719X-RAY DIFFRACTION100
3.24-4.080.17491480.15412754X-RAY DIFFRACTION99.97
4.08-38.270.16041450.15292869X-RAY DIFFRACTION99.87

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