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- PDB-5kre: Covalent inhibitor of LYPLAL1 -

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Basic information

Entry
Database: PDB / ID: 5kre
TitleCovalent inhibitor of LYPLAL1
ComponentsLysophospholipase-like protein 1
KeywordsHYDROLASE/HYDROLASE inhibitor / LYPLAL1 / serine hydrolase / covalent inhibitor / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


palmitoyl-(protein) hydrolase activity / palmitoyl[protein] hydrolase / lysophospholipase activity / carboxylic ester hydrolase activity / hydrolase activity, acting on ester bonds / negative regulation of cGAS/STING signaling pathway / cytosol / cytoplasm
Similarity search - Function
: / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2~{R})-2-phenylpiperidine-1-carbaldehyde / NITRATE ION / Lysophospholipase-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPandit, J.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Discovery of a Selective Covalent Inhibitor of Lysophospholipase-like 1 (LYPLAL1) as a Tool to Evaluate the Role of this Serine Hydrolase in Metabolism.
Authors: Ahn, K. / Boehm, M. / Brown, M.F. / Calloway, J. / Che, Y. / Chen, J. / Fennell, K.F. / Geoghegan, K.F. / Gilbert, A.M. / Gutierrez, J.A. / Kalgutkar, A.S. / Lanba, A. / Limberakis, C. / ...Authors: Ahn, K. / Boehm, M. / Brown, M.F. / Calloway, J. / Che, Y. / Chen, J. / Fennell, K.F. / Geoghegan, K.F. / Gilbert, A.M. / Gutierrez, J.A. / Kalgutkar, A.S. / Lanba, A. / Limberakis, C. / Magee, T.V. / O'Doherty, I. / Oliver, R. / Pabst, B. / Pandit, J. / Parris, K. / Pfefferkorn, J.A. / Rolph, T.P. / Patel, R. / Schuff, B. / Shanmugasundaram, V. / Starr, J.T. / Varghese, A.H. / Vera, N.B. / Vernochet, C. / Yan, J.
History
DepositionJul 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Oct 4, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysophospholipase-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7733
Polymers26,5221
Non-polymers2512
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.410, 61.440, 75.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysophospholipase-like protein 1


Mass: 26521.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYPLAL1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5VWZ2, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical ChemComp-6WG / (2~{R})-2-phenylpiperidine-1-carbaldehyde


Mass: 189.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15NO
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Reservoir: 22% PEG 3350 and 100mM ammonium nitrate, Protein Buffer: 20mM Tris pH 8.0, 30mM NaCl, 1mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 15495 / % possible obs: 99.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 23.43 Å2 / Rmerge(I) obs: 0.095 / Χ2: 0.739 / Net I/av σ(I): 16.391 / Net I/σ(I): 5 / Num. measured all: 91849
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.0340.302195.9
2.03-2.074.70.263198.3
2.07-2.115.20.244199.6
2.11-2.155.60.244199.9
2.15-2.25.70.221100
2.2-2.255.80.219199.9
2.25-2.315.70.1951100
2.31-2.376.10.181199.9
2.37-2.446.20.1631100
2.44-2.526.50.1631100
2.52-2.616.50.1521100
2.61-2.716.30.1311100
2.71-2.846.10.1161100
2.84-2.996.20.1041100
2.99-3.176.70.0931100
3.17-3.426.50.084199.9
3.42-3.766.10.0741100
3.76-4.316.40.066199.9
4.31-5.436.10.0641100
5.43-505.80.067199.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
BUSTER-TNT2.11.5refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U0V

3u0v


Resolution: 2→40.22 Å / Cor.coef. Fo:Fc: 0.9373 / Cor.coef. Fo:Fc free: 0.9081 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.18 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 1030 6.67 %RANDOM
Rwork0.1653 ---
obs0.1684 15450 99.29 %-
Displacement parametersBiso max: 98.81 Å2 / Biso mean: 24.46 Å2 / Biso min: 10.86 Å2
Baniso -1Baniso -2Baniso -3
1--2.0744 Å20 Å20 Å2
2--8.045 Å20 Å2
3----5.9706 Å2
Refine analyzeLuzzati coordinate error obs: 0.191 Å
Refinement stepCycle: final / Resolution: 2→40.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 32 153 1940
Biso mean--22.15 36.23 -
Num. residues----224
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d636SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes278HARMONIC5
X-RAY DIFFRACTIONt_it1848HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion236SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2293SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1848HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2514HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion18.18
LS refinement shellResolution: 2→2.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2035 190 7.15 %
Rwork0.1683 2467 -
all0.1708 2657 -
obs--99.29 %

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