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- PDB-4uuq: Crystal structure of human mono-glyceride lipase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4uuq
TitleCrystal structure of human mono-glyceride lipase in complex with SAR127303
ComponentsMONOGLYCERIDE LIPASE
KeywordsHYDROLASE
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 / acylglycerol 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 / acylglycerol 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-64D / Monoglyceride lipase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsGriebel, G. / Pichat, P. / Beeske, S. / Leroy, T. / Redon, N. / Francon, D. / Bert, L. / Even, L. / Lopez-Grancha, M. / Tolstykh, T. ...Griebel, G. / Pichat, P. / Beeske, S. / Leroy, T. / Redon, N. / Francon, D. / Bert, L. / Even, L. / Lopez-Grancha, M. / Tolstykh, T. / Sun, F. / Yu, Q. / Brittain, S. / Arlt, H. / He, T. / Zhang, B. / Wiederschain, D. / Bertrand, T. / Houtman, J. / Rak, A. / Vallee, F. / Michot, N. / Auge, F. / Menet, V. / Bergis, O.E. / George, P. / Avenet, P. / Mikol, V. / Didier, M. / Escoubet, J.
CitationJournal: Sci.Rep. / Year: 2015
Title: Selective Blockade of the Hydrolysis of the Endocannabinoid 2-Arachidonoylglycerol Impairs Learning and Memory Performance While Producing Antinociceptive Activity in Rodents.
Authors: Griebel, G. / Pichat, P. / Beeske, S. / Leroy, T. / Redon, N. / Jacquet, A. / Francon, D. / Bert, L. / Even, L. / Lopez-Grancha, M. / Tolstykh, T. / Sun, F. / Yu, Q. / Brittain, S. / Arlt, H. ...Authors: Griebel, G. / Pichat, P. / Beeske, S. / Leroy, T. / Redon, N. / Jacquet, A. / Francon, D. / Bert, L. / Even, L. / Lopez-Grancha, M. / Tolstykh, T. / Sun, F. / Yu, Q. / Brittain, S. / Arlt, H. / He, T. / Zhang, B. / Wiederschain, D. / Bertrand, T. / Houtmann, J. / Rak, A. / Vallee, F. / Michot, N. / Auge, F. / Menet, V. / Bergis, O.E. / George, P. / Avenet, P. / Mikol, V. / Didier, M. / Escoubet, J.
History
DepositionJul 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MONOGLYCERIDE LIPASE
B: MONOGLYCERIDE LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2514
Polymers70,5852
Non-polymers6662
Water4,342241
1
A: MONOGLYCERIDE LIPASE
hetero molecules

A: MONOGLYCERIDE LIPASE
hetero molecules

A: MONOGLYCERIDE LIPASE
hetero molecules

A: MONOGLYCERIDE LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5018
Polymers141,1704
Non-polymers1,3314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area5850 Å2
ΔGint-38.7 kcal/mol
Surface area46120 Å2
MethodPISA
2
B: MONOGLYCERIDE LIPASE
hetero molecules

B: MONOGLYCERIDE LIPASE
hetero molecules

B: MONOGLYCERIDE LIPASE
hetero molecules

B: MONOGLYCERIDE LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5018
Polymers141,1704
Non-polymers1,3314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5380 Å2
ΔGint-38.6 kcal/mol
Surface area45240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.250, 126.260, 138.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein MONOGLYCERIDE LIPASE / MGL / HU-K5 / LYSOPHOSPHOLIPASE HOMOLOG / LYSOPHOSPHOLIPASE-LIKE / MONOACYLGLYCEROL LIPASE / MAGL / MGLL


Mass: 35292.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99685, acylglycerol lipase
#2: Chemical ChemComp-64D / 4-({[(4-chlorophenyl)sulfonyl]amino}methyl)piperidine-1-carboxylic acid


Mass: 332.803 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17ClN2O4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 3.02 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growTemperature: 277 K / pH: 6 / Details: MES BUFFER 50MM PH6.0, MPD 40%(V/V) AT 4C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9814
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 20, 2008 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 2.36→73.32 Å / Num. obs: 20609 / % possible obs: 95.2 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Biso Wilson estimate: 52.356 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 17.7
Reflection shellResolution: 2.36→2.5 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.6 / % possible all: 97.1

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Processing

Software
NameVersionClassification
BUSTER-TNT2.5.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JW8

3jw8


Resolution: 2.36→73.32 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: COVALENT BONDING BETWEEN CLEAVED LIGAND AND SERINE 132
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 2986 10.09 %RANDOM
Rwork0.2099 ---
obs0.215 29604 94.14 %-
Displacement parametersBiso mean: 46.06 Å2
Baniso -1Baniso -2Baniso -3
1-7.53157145 Å20 Å20 Å2
2--3.22051862 Å20 Å2
3----10.75209006 Å2
Refinement stepCycle: LAST / Resolution: 2.36→73.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4404 0 40 241 4685
LS refinement shellResolution: 2.36→2.5 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2628 464 9.69 %
Rwork0.2185 4326 -
all0.2228 4790 -
obs--94.14 %

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