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- PDB-5jad: Compound binding to Human Lipoprotein-Associated Phospholipase A2... -

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Basic information

Entry
Database: PDB / ID: 5jad
TitleCompound binding to Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2)discovered through fragment screening
ComponentsPlatelet-activating factor acetylhydrolase
KeywordsHYDROLASE / phospholipase / lipid metabolism
Function / homology
Function and homology information


plasma lipoprotein particle oxidation / platelet activating factor catabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase / calcium-independent phospholipase A2 activity / platelet activating factor metabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase activity / phosphatidylcholine catabolic process / lipid oxidation / low-density lipoprotein particle / high-density lipoprotein particle ...plasma lipoprotein particle oxidation / platelet activating factor catabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase / calcium-independent phospholipase A2 activity / platelet activating factor metabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase activity / phosphatidylcholine catabolic process / lipid oxidation / 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
benzenesulfonamide / Platelet-activating factor acetylhydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsDay, P.J. / Woolford, A.J.-A.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered through X-ray Fragment Screening.
Authors: Woolford, A.J. / Pero, J.E. / Aravapalli, S. / Berdini, V. / Coyle, J.E. / Day, P.J. / Dodson, A.M. / Grondin, P. / Holding, F.P. / Lee, L.Y. / Li, P. / Manas, E.S. / Marino, J. / Martin, A. ...Authors: Woolford, A.J. / Pero, J.E. / Aravapalli, S. / Berdini, V. / Coyle, J.E. / Day, P.J. / Dodson, A.M. / Grondin, P. / Holding, F.P. / Lee, L.Y. / Li, P. / Manas, E.S. / Marino, J. / Martin, A.C. / McCleland, B.W. / McMenamin, R.L. / Murray, C.W. / Neipp, C.E. / Page, L.W. / Patel, V.K. / Potvain, F. / Rich, S. / Rivero, R.A. / Smith, K. / Somers, D.O. / Trottet, L. / Velagaleti, R. / Williams, G. / Xie, R.
History
DepositionApr 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)44,4985
Polymers44,2031
Non-polymers2954
Water2,576143
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-14 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.970, 91.029, 51.191
Angle α, β, γ (deg.)90.00, 112.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-501-

MG

21A-718-

HOH

31A-725-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G7, PAFAH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q13093, 1-alkyl-2-acetylglycerophosphocholine esterase

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Non-polymers , 5 types, 147 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-FB2 / benzenesulfonamide


Mass: 157.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7NO2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1.2M NaCl, 0.1M HEPES/NaOHpH=7.4, 28.8%w/v PEG 3350
PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5417 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 15, 2010 / Details: VariMax VHF Arc)Sec optic
RadiationMonochromator: VariMax VHF Arc)Sec optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.05→64 Å / Num. obs: 103331 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 28.81 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.6
Reflection shellResolution: 2.05→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.3 / % possible all: 88.7

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
SCALAdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.05→32.31 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.869 / SU R Cruickshank DPI: 0.248 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.244 / SU Rfree Blow DPI: 0.212 / SU Rfree Cruickshank DPI: 0.215
Details: Buster refinement was interspersed with rounds of rebuilding with COOT
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1303 5.09 %RANDOM
Rwork0.245 ---
obs0.247 25600 96.9 %-
Displacement parametersBiso mean: 33.676 Å2
Baniso -1Baniso -2Baniso -3
1--5.3006 Å20 Å2-1.7419 Å2
2--4.7839 Å20 Å2
3---0.5167 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.05→32.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2973 0 16 143 3132
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0123070HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084155HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1067SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes457HARMONIC16
X-RAY DIFFRACTIONt_it3070HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion7.18
X-RAY DIFFRACTIONt_other_torsion18.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion392SEMIHARMONIC5
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_contact3692SEMIHARMONIC4
LS refinement shellHighest resolution: 2.05 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.402 127 5.04 %
Rwork0.324 2395 -
obs--85.06 %
Refinement TLS params.Method: refined / Origin x: 30.0021 Å / Origin y: 14.7021 Å / Origin z: 0.8666 Å
111213212223313233
T-0.2971 Å20.0156 Å2-0.0338 Å2-0.0072 Å2-0.0384 Å2---0.0808 Å2
L3.4132 °20.3331 °20.6517 °2-1.2369 °2-0.0243 °2--1.2011 °2
S-0.0136 Å °0.0193 Å °0.1685 Å °0.0258 Å °-0.0308 Å °0.0964 Å °0.0065 Å °0.0518 Å °0.0444 Å °
Refinement TLS groupSelection details: { A|55 - A|425 }

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