Structure of PDB 3u8d Chain A

Receptor sequence
>3u8dA (length=124) Species: 9606 (Homo sapiens) [Search protein sequence]
NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCC
YKRLEKRGCGTKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFAR
NKTTYNKKYQYYSNKHCRGSTPRC
3D structure
PDB3u8d Selective Inhibition of Human Group IIA-secreted Phospholipase A2 (hGIIA) Signaling Reveals Arachidonic Acid Metabolism Is Associated with Colocalization of hGIIA to Vimentin in Rheumatoid Synoviocytes.
ChainA
Resolution1.805 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) H27 G29 G31 H47 D48 Y51 Y66 D91
Catalytic site (residue number reindexed from 1) H27 G29 G31 H47 D48 Y51 Y66 D91
Enzyme Commision number 3.1.1.4: phospholipase A2.
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 U8D A L2 F5 H6 Y21 C28 G29 G31 H47 D48 K62 F98 L2 F5 H6 Y21 C28 G29 G31 H47 D48 K62 F98 PDBbind-CN: -logKd/Ki=6.33,IC50=0.47uM
BindingDB: IC50=470nM
BS02 CA A H27 G29 G31 D48 H27 G29 G31 D48
BS03 CA A F23 G25 Y112 N114 F23 G25 Y112 N114
Gene Ontology
Molecular Function
GO:0004623 phospholipase A2 activity
GO:0005509 calcium ion binding
GO:0005543 phospholipid binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0047498 calcium-dependent phospholipase A2 activity
Biological Process
GO:0006629 lipid metabolic process
GO:0006644 phospholipid metabolic process
GO:0006954 inflammatory response
GO:0010744 positive regulation of macrophage derived foam cell differentiation
GO:0016042 lipid catabolic process
GO:0031640 killing of cells of another organism
GO:0034374 low-density lipoprotein particle remodeling
GO:0036335 intestinal stem cell homeostasis
GO:0042130 negative regulation of T cell proliferation
GO:0042742 defense response to bacterium
GO:0046337 phosphatidylethanolamine metabolic process
GO:0046470 phosphatidylcholine metabolic process
GO:0046473 phosphatidic acid metabolic process
GO:0050482 arachidonate secretion
GO:0050729 positive regulation of inflammatory response
GO:0050830 defense response to Gram-positive bacterium
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:1902563 regulation of neutrophil activation
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005886 plasma membrane
GO:0030141 secretory granule
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3u8d, PDBe:3u8d, PDBj:3u8d
PDBsum3u8d
PubMed23482564
UniProtP14555|PA2GA_HUMAN Phospholipase A2, membrane associated (Gene Name=PLA2G2A)

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