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

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Entry
Database: PDB / ID: 5jan
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-6HP / Platelet-activating factor acetylhydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.12 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)44,5265
Polymers44,2031
Non-polymers3234
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-21 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.373, 92.080, 48.273
Angle α, β, γ (deg.)90.00, 112.60, 90.00
Int Tables number5
Space group name H-MC121

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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
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-6HP / 1,3-dimethyl-6-(2-methylpropoxy)pyrimidine-2,4(1H,3H)-dione


Mass: 212.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 1.0M NaCl, 0.1M HEPES/NaOHpH=7.4, 28.8%w/v PEG 3350

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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 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.12→46.33 Å / Num. obs: 21778 / % possible obs: 99.2 % / Redundancy: 3.6 % / Net I/σ(I): 7.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
d*TREKdata reduction
SCALAdata scaling
RefinementResolution: 2.12→46.33 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / SU B: 16.474 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.219 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26693 1172 5.1 %RANDOM
Rwork0.22291 ---
obs0.22519 21778 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.96 Å2
Baniso -1Baniso -2Baniso -3
1--2.67 Å2-0 Å20.78 Å2
2---2.14 Å20 Å2
3---3.09 Å2
Refinement stepCycle: 1 / Resolution: 2.12→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 18 131 3127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193071
X-RAY DIFFRACTIONr_bond_other_d0.0020.022904
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9464154
X-RAY DIFFRACTIONr_angle_other_deg0.9322.9886684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8055372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83623.865148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23315.028532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9841518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2442
X-RAY DIFFRACTIONr_gen_planes_refined00.0213472
X-RAY DIFFRACTIONr_gen_planes_other00.02738
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0573.1391485
X-RAY DIFFRACTIONr_mcbond_other1.0363.1351484
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3473.5461584
X-RAY DIFFRACTIONr_scbond_other1.3473.5491585
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.3967.2981071
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.117→2.172 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 95 -
Rwork0.312 1567 -
obs--98.17 %
Refinement TLS params.Method: refined / Origin x: 30.7183 Å / Origin y: 14.6937 Å / Origin z: 1.0399 Å
111213212223313233
T0.126 Å20.0013 Å20.0471 Å2-0.1333 Å2-0.0235 Å2--0.027 Å2
L2.4734 °2-0.3773 °20.304 °2-2.2689 °2-0.3996 °2--1.6822 °2
S0.0407 Å °-0.0469 Å °0.0695 Å °0.0124 Å °-0.0338 Å °0.0995 Å °-0.035 Å °-0.1306 Å °-0.007 Å °

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