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- PDB-5zun: Crystal structure of human monoacylglycerol lipase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5zun
TitleCrystal structure of human monoacylglycerol lipase in complex with compound 3l
ComponentsMonoglyceride lipase
KeywordsHYDROLASE/INHIBITOR / MONOACYLGLYCEROL LIPASE / HYDROLASE-INHIBITOR complex
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 / arachidonic acid 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 / arachidonic acid 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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9JX / Monoglyceride lipase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSogabe, S. / Zama, Y. / Lane, W. / Snell, G.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Design, Synthesis, and Evaluation of Piperazinyl Pyrrolidin-2-ones as a Novel Series of Reversible Monoacylglycerol Lipase Inhibitors
Authors: Aida, J. / Fushimi, M. / Kusumoto, T. / Sugiyama, H. / Arimura, N. / Ikeda, S. / Sasaki, M. / Sogabe, S. / Aoyama, K. / Koike, T.
History
DepositionMay 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)34,52812
Polymers33,3351
Non-polymers1,19311
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.149, 127.224, 60.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

21A-707-

HOH

31A-776-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 33335.254 Da / Num. of mol.: 1 / Mutation: K36A, L169S. L176S
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

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Non-polymers , 5 types, 308 molecules

#2: Chemical ChemComp-9JX / (4R)-1-(2'-chloro[1,1'-biphenyl]-3-yl)-4-[4-(1,3-thiazole-2-carbonyl)piperazin-1-yl]pyrrolidin-2-one


Mass: 466.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23ClN4O2S
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M Bis-Tris, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 78596 / % possible obs: 98 % / Redundancy: 6.9 % / Rsym value: 0.074 / Net I/σ(I): 22.6
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3064 / Rsym value: 0.852 / % possible all: 77.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PE6

3pe6


Resolution: 1.35→40 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.479 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.042 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16008 3916 5 %RANDOM
Rwork0.14693 ---
obs0.14758 74657 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.803 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å2-0 Å2
2---0.69 Å20 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 1.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 78 297 2613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0152468
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172291
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.7653357
X-RAY DIFFRACTIONr_angle_other_deg0.551.7325380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8325321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.75819.04884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09715370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1161514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02456
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8341.0071194
X-RAY DIFFRACTIONr_mcbond_other0.8331.0081195
X-RAY DIFFRACTIONr_mcangle_it1.4241.5091501
X-RAY DIFFRACTIONr_mcangle_other1.4281.5111502
X-RAY DIFFRACTIONr_scbond_it1.2841.1851274
X-RAY DIFFRACTIONr_scbond_other1.2821.1851274
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0071.6921840
X-RAY DIFFRACTIONr_long_range_B_refined4.35313.6632766
X-RAY DIFFRACTIONr_long_range_B_other4.00112.9482696
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 243 -
Rwork0.272 4314 -
obs--77.94 %
Refinement TLS params.Method: refined / Origin x: -17.9288 Å / Origin y: 20.0718 Å / Origin z: -1.3645 Å
111213212223313233
T0.0084 Å20.0047 Å20.0041 Å2-0.0042 Å20.0026 Å2--0.0033 Å2
L0.2329 °2-0.0208 °2-0.0394 °2-0.6617 °20.1407 °2--0.6598 °2
S-0.0186 Å °-0.0239 Å °-0.0025 Å °0.0038 Å °0.001 Å °0.0065 Å °-0.0132 Å °0.0154 Å °0.0176 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 295
2X-RAY DIFFRACTION1A401

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