Structure of PDB 5lyy Chain A

Receptor sequence
>5lyyA (length=371) Species: 9606 (Homo sapiens) [Search protein sequence]
KIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYF
WGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLG
AFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWL
YLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFD
MEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGD
EVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNF
ADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQ
WDCLIEGDDENLIPGTNINTT
3D structure
PDB5lyy Fragment-Based Approach to the Development of an Orally Bioavailable Lactam Inhibitor of Lipoprotein-Associated Phospholipase A2 (Lp-PLA2).
ChainA
Resolution2.17 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.1.1.47: 1-alkyl-2-acetylglycerophosphocholine esterase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 7BJ A F110 G152 L153 G154 L159 S273 F274 W298 F322 H351 Q352 F357 F56 G98 L99 G100 L105 S219 F220 W244 F268 H297 Q298 F303 MOAD: ic50=14uM
PDBbind-CN: -logKd/Ki=4.85,IC50=14uM
BindingDB: IC50=14000nM
Gene Ontology
Molecular Function
GO:0003847 1-alkyl-2-acetylglycerophosphocholine esterase activity
GO:0005515 protein binding
GO:0005543 phospholipid binding
GO:0016787 hydrolase activity
GO:0016788 hydrolase activity, acting on ester bonds
GO:0047499 calcium-independent phospholipase A2 activity
Biological Process
GO:0009395 phospholipid catabolic process
GO:0016486 peptide hormone processing
GO:0034374 low-density lipoprotein particle remodeling
GO:0034440 lipid oxidation
GO:0034441 plasma lipoprotein particle oxidation
GO:0034638 phosphatidylcholine catabolic process
GO:0046469 platelet activating factor metabolic process
GO:0050729 positive regulation of inflammatory response
GO:0062234 platelet activating factor catabolic process
GO:0090026 positive regulation of monocyte chemotaxis
Cellular Component
GO:0005576 extracellular region
GO:0034362 low-density lipoprotein particle
GO:0034364 high-density lipoprotein particle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5lyy, PDBe:5lyy, PDBj:5lyy
PDBsum5lyy
PubMed27933945
UniProtQ13093|PAFA_HUMAN Platelet-activating factor acetylhydrolase (Gene Name=PLA2G7)

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