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- PDB-5jap: Exploitation of a Novel Binding Pocket in Human Lipoprotein-Assoc... -

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Entry
Database: PDB / ID: 5jap
TitleExploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered Through X-Ray 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
Chem-6HZ / Platelet-activating factor acetylhydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.46 Å
AuthorsDay, P.J.
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 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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)44,6345
Polymers44,2031
Non-polymers4314
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-15 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.927, 90.661, 51.303
Angle α, β, γ (deg.)90.00, 111.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-501-

CA

21A-678-

HOH

31A-868-

HOH

41A-939-

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)
References: UniProt: Q13093, 1-alkyl-2-acetylglycerophosphocholine esterase

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Non-polymers , 5 types, 369 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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-6HZ / (2,5-dihydro-1H-pyrrol-1-yl)(2',6-dimethyl[1,1'-biphenyl]-3-yl)methanone


Mass: 277.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19NO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 28.0%w/v PEG 3350, 0.1M HEPES/NaOHpH=7.4, 1.3M NaCl

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.46→44.24 Å / Num. obs: 15287 / % possible obs: 98.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 49.77 Å2 / Net I/σ(I): 9

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
d*TREKdata reduction
SCALAdata scaling
RefinementResolution: 2.46→44.24 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.889 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.595 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.042 / SU Rfree Blow DPI: 0.292 / SU Rfree Cruickshank DPI: 0.285
RfactorNum. reflection% reflectionSelection details
Rfree0.246 779 5.1 %RANDOM
Rwork0.173 ---
obs0.177 15287 98.5 %-
Displacement parametersBiso mean: 37.331 Å2
Baniso -1Baniso -2Baniso -3
1-1.9462 Å20 Å2-2.0862 Å2
2---7.5794 Å20 Å2
3---5.6332 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: 1 / Resolution: 2.46→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2973 0 27 365 3365
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113097HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084203HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1075SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes462HARMONIC16
X-RAY DIFFRACTIONt_it3097HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion6.9
X-RAY DIFFRACTIONt_other_torsion19.04
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_contact3856SEMIHARMONIC4
LS refinement shellResolution: 2.46→2.63 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.347 135 4.89 %
Rwork0.229 2624 -
obs--99.07 %
Refinement TLS params.Method: refined / Origin x: 30.5112 Å / Origin y: 14.8788 Å / Origin z: 0.9311 Å
111213212223313233
T-0.2083 Å20.0075 Å20.007 Å2--0.1154 Å2-0.0279 Å2---0.0039 Å2
L1.7389 °20.0906 °20.3296 °2-1.8287 °2-0.2717 °2--1.3643 °2
S0.0379 Å °-0.0693 Å °0.0314 Å °0.057 Å °-0.0485 Å °0.0975 Å °-0.0388 Å °-0.0345 Å °0.0106 Å °
Refinement TLS groupSelection details: { A|55 - A|425 }

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