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- PDB-3pe6: Crystal Structure of a soluble form of human MGLL in complex with... -

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Basic information

Entry
Database: PDB / ID: 3pe6
TitleCrystal Structure of a soluble form of human MGLL in complex with an inhibitor
ComponentsMonoglyceride lipase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / alpha-beta hydrolase fold / Lipase / 2-arachidonyl-glycerol / Membrane associated / HYDROLASE / HYDROLASE-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-ZYH / Monoglyceride lipase / Monoglyceride lipase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSchubert, C. / Schalk-Hih, C.
CitationJournal: Protein Sci. / Year: 2011
Title: Crystal structure of a soluble form of human monoglyceride lipase in complex with an inhibitor at 1.35 A resolution.
Authors: Schalk-Hihi, C. / Schubert, C. / Alexander, R. / Bayoumy, S. / Clemente, J.C. / Deckman, I. / DesJarlais, R.L. / Dzordzorme, K.C. / Flores, C.M. / Grasberger, B. / Kranz, J.K. / Lewandowski, ...Authors: Schalk-Hihi, C. / Schubert, C. / Alexander, R. / Bayoumy, S. / Clemente, J.C. / Deckman, I. / DesJarlais, R.L. / Dzordzorme, K.C. / Flores, C.M. / Grasberger, B. / Kranz, J.K. / Lewandowski, F. / Liu, L. / Ma, H. / Maguire, D. / Macielag, M.J. / McDonnell, M.E. / Mezzasalma Haarlander, T. / Miller, R. / Milligan, C. / Reynolds, C. / Kuo, L.C.
History
DepositionOct 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)33,6382
Polymers33,1911
Non-polymers4471
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.947, 128.145, 60.602
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-475-

HOH

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Components

#1: Protein Monoglyceride lipase / MGLL protein / isoform CRA_b / cDNA / FLJ96595 / Homo sapiens monoglyceride lipase (MGLL) / mRNA


Mass: 33191.125 Da / Num. of mol.: 1 / Fragment: Short form of MGLL (UNP residues 11 to 313) / Mutation: K36A, L169S, L176S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGLL, hCG_40840 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6IBG9, UniProt: Q99685*PLUS, acylglycerol lipase
#2: Chemical ChemComp-ZYH / (2-cyclohexyl-1,3-benzoxazol-6-yl){3-[4-(pyrimidin-2-yl)piperazin-1-yl]azetidin-1-yl}methanone


Mass: 446.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H30N6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEGMME5000 MES glucopyranoside, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 79919 / Num. obs: 79919 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.7 / Redundancy: 2.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 34.2
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 1.76 / Num. unique all: 4728 / % possible all: 53.3

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A8Q

1a8q


Resolution: 1.35→30.42 Å / SU ML: 1.17 / Isotropic thermal model: partially anisotropic / Cross valid method: THROUGHOUT / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1466 1794 2.51 %Random
Rwork0.114 ---
obs0.1148 71433 88.91 %-
all-71433 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.862 Å2 / ksol: 0.464 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.5786 Å2-0 Å2-0 Å2
2---2.3961 Å20 Å2
3----0.7641 Å2
Refinement stepCycle: LAST / Resolution: 1.35→30.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 33 360 2631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144904
X-RAY DIFFRACTIONf_angle_d1.4358951
X-RAY DIFFRACTIONf_dihedral_angle_d17.8771279
X-RAY DIFFRACTIONf_chiral_restr0.104383
X-RAY DIFFRACTIONf_plane_restr0.011742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.38650.32191000.21933696X-RAY DIFFRACTION63
1.3865-1.42730.24181120.16434306X-RAY DIFFRACTION72
1.4273-1.47340.19381230.13524695X-RAY DIFFRACTION79
1.4734-1.5260.18831280.1124923X-RAY DIFFRACTION82
1.526-1.58710.14311300.09695166X-RAY DIFFRACTION86
1.5871-1.65940.13531400.0885463X-RAY DIFFRACTION92
1.6594-1.74680.10771430.08425747X-RAY DIFFRACTION96
1.7468-1.85630.12891520.08455851X-RAY DIFFRACTION97
1.8563-1.99960.1351520.08745904X-RAY DIFFRACTION98
1.9996-2.20070.12081540.08715980X-RAY DIFFRACTION99
2.2007-2.5190.11351540.09266004X-RAY DIFFRACTION99
2.519-3.17320.12881570.10596081X-RAY DIFFRACTION100
3.1732-30.42820.15721490.14485823X-RAY DIFFRACTION92

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