Structure of PDB 5ebe Chain A

Receptor sequence

>5ebeA (length=418) Species: 9606 (Homo sapiens)

PPPAIGQFWHVTDLHLDPTYHITDDHTKVCASSKGANASNPGPFGDVLCD
SPYQLILSAFDFIKNSGQEASFMIWTGDSPPHVPVPELSTDTVINVITNM
TTTIQSLFPNLQVFPALGNHDYWPQDQLPVVTSKVYNAVANLWKPWLDEE
AISTLRKGGFYSQKVTTNPNLRIISLNTNLYYGPNIMTLNKTDPANQFEW
LESTLNNSQQNKEKVYIIAHVPVGYLPSSQNITAMREYYNEKLIDIFQKY
SDVIAGQFYGHTHRDSIMVLSDKKGSPVNSLFVAPAVTPVKSVLEKQTNN
PGIRLFQYDPRDYKLLDMLQYYLNLTEANLKGESIWKLEYILTQTYDIED
LQPESLYGLAKQFTILDSKQFIKYYNYFFVSYDSSVTCDKTCKAFQICAI
MNLDNISYADCLKQLYIK

3D structure

• PDB: 5ebe The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a - an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity.
• Chain: A
• Resolution: 3.0 Å

Enzymatic activity

• Enzyme Commision number: 3.1.4.-
  3.6.1.15: nucleoside-triphosphate phosphatase.

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	ZN	A	D110 N151 H252 H293	D78 N119 H220 H261
BS02	ZN	A	D45 H47 D110 H295	D13 H15 D78 H263
BS03	C5P	A	D110 H114 N151 H152 H293 H295 V322 K323	D78 H82 N119 H120 H261 H263 V290 K291

Gene Ontology

Molecular Function

• GO:0004767 sphingomyelin phosphodiesterase activity
• GO:0005515 protein binding
• GO:0008081 phosphoric diester hydrolase activity
• GO:0008270 zinc ion binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006685 sphingomyelin catabolic process
• GO:0009143 nucleoside triphosphate catabolic process
• GO:0160049 negative regulation of cGAS/STING signaling pathway

Cellular Component

• GO:0005576 extracellular region
• GO:0005615 extracellular space
• GO:0070062 extracellular exosome

External links

• PDB: RCSB:5ebe, PDBe:5ebe, PDBj:5ebe
• PDBsum: 5ebe
• PubMed: 26783088
• UniProt: Q92484|ASM3A_HUMAN Cyclic GMP-AMP phosphodiesterase SMPDL3A (Gene Name=SMPDL3A)