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- PDB-5lp1: CRYSTAL STRUCTURE OF HUMAN LIPOPROTEIN-ASSOCIATED PHOSPHOLIPASE A... -

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Basic information

Entry
Database: PDB / ID: 5lp1
TitleCRYSTAL STRUCTURE OF HUMAN LIPOPROTEIN-ASSOCIATED PHOSPHOLIPASE A2 IN COMPLEX WITH A [1.1.1]BICYCLOPENTANE-CONTAINING INHIBITOR AT 1.91A RESOLUTION.
ComponentsPlatelet-activating factor acetylhydrolase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PLASMA PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE / SECRETED PROTEIN / ALPHA/BETA-HYDROLASE-FOLD / LDL-BOUND / LIPOPROTEIN ASSOCIATED PHOSPHOLIPASE A2 / LP-PLA2 / GROUP VIIA PLA2 / GLYCOPROTEIN / HYDROLASE / LIPID DEGRADATION / POLYMORPHISM / SECRETED / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


plasma lipoprotein particle oxidation / platelet activating factor catabolic process / calcium-independent phospholipase A2 activity / 1-alkyl-2-acetylglycerophosphocholine esterase / platelet activating factor metabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase activity / lipid oxidation / phosphatidylcholine catabolic process / low-density lipoprotein particle / high-density lipoprotein particle ...plasma lipoprotein particle oxidation / platelet activating factor catabolic process / calcium-independent phospholipase A2 activity / 1-alkyl-2-acetylglycerophosphocholine esterase / platelet activating factor metabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase activity / lipid oxidation / phosphatidylcholine catabolic process / low-density lipoprotein particle / high-density lipoprotein particle / low-density lipoprotein particle remodeling / positive regulation of monocyte chemotaxis / peptide hormone processing / hydrolase activity, acting on ester bonds / Synthesis, secretion, and deacylation of Ghrelin / phospholipid binding / positive regulation of inflammatory response / extracellular region
Similarity search - Function
Platelet-activating factor acetylhydrolase, eucaryote / Platelet-activating factor acetylhydrolase, isoform II / Lipases, serine active site. / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-71H / Platelet-activating factor acetylhydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.91 Å
AuthorsSomers, D.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Investigation of a Bicyclo[1.1.1]pentane as a Phenyl Replacement within an LpPLA2 Inhibitor.
Authors: Measom, N.D. / Down, K.D. / Hirst, D.J. / Jamieson, C. / Manas, E.S. / Patel, V.K. / Somers, D.O.
History
DepositionAug 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.2May 1, 2024Group: 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

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Assembly

Deposited unit
A: Platelet-activating factor acetylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9294
Polymers44,2031
Non-polymers7263
Water5,981332
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-16 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.280, 91.560, 51.650
Angle α, β, γ (deg.)90.000, 111.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21A-833-

HOH

31A-885-

HOH

41A-904-

HOH

51A-914-

HOH

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Components

#1: Protein Platelet-activating factor acetylhydrolase / PAF acetylhydrolase / 1-alkyl-2-acetylglycerophosphocholine esterase / 2-acetyl-1- ...PAF acetylhydrolase / 1-alkyl-2-acetylglycerophosphocholine esterase / 2-acetyl-1-alkylglycerophosphocholine esterase / Group-VIIA phospholipase A2 / gVIIA-PLA2 / LDL-associated phospholipase A2 / LDL-PLA(2) / PAF 2-acylhydrolase


Mass: 44203.129 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 46-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G7, PAFAH / Production host: Escherichia coli (E. coli)
References: UniProt: Q13093, 1-alkyl-2-acetylglycerophosphocholine esterase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-71H / ~{N}-[2-(diethylamino)ethyl]-2-[2-[(4-fluorophenyl)methylsulfanyl]-4-oxidanylidene-5~{H}-cyclopenta[d]pyrimidin-1-yl]-~{N}-[[3-[4-(trifluoromethyl)phenyl]-1-bicyclo[1.1.1]pentanyl]methyl]ethanamide


Mass: 654.760 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H38F4N4O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: Sodium chloride, PEG 3350, HEPES.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.91→47.93 Å / Num. obs: 33162 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.912 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.094 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.91-1.983.20.6241.70.672192.5
7.4-47.933.50.0716.80.991199.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.9data scaling
REFMACphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: In-house coordinates

Resolution: 1.91→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.479 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1389 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.124
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1922 1651 5 %RANDOM
Rwork0.1623 ---
obs0.1637 31474 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.72 Å2 / Biso mean: 35.812 Å2 / Biso min: 20.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å2-0 Å20.44 Å2
2--0.06 Å20 Å2
3---0.53 Å2
Refinement stepCycle: final / Resolution: 1.91→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2959 0 48 332 3339
Biso mean--36.99 47.45 -
Num. residues----370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193175
X-RAY DIFFRACTIONr_bond_other_d0.0020.022982
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9464317
X-RAY DIFFRACTIONr_angle_other_deg0.90636876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4945391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30223.851148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.6915542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8571519
X-RAY DIFFRACTIONr_chiral_restr0.0850.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213747
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02766
X-RAY DIFFRACTIONr_mcbond_it2.2936.6011534
X-RAY DIFFRACTIONr_mcbond_other2.2926.6041535
X-RAY DIFFRACTIONr_mcangle_it3.29111.1171936
LS refinement shellResolution: 1.91→1.959 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 112 -
Rwork0.311 2097 -
all-2209 -
obs--90.42 %

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