Structure of PDB 5ebe Chain C

Receptor sequence
>5ebeC (length=415) Species: 9606 (Homo sapiens) [Search protein sequence]
PPPAIGQFWHVTDLHLDPTYHITDDHTKVCASSKGANASNPGPFGDVLCD
SPYQLILSAFDFIKNSGQEASFMIWTGDSPPHVPVPELSTDTVINVITNM
TTTIQSLFPNLQVFPALGNHDYWPQDQLPVVTSKVYNAVANLWKPWLDEE
AISTLRKGGFYSQKVTTNPNLRIISLNTNLYYGPNIMTLNKTDPANQFEW
LESTLNNSQQNKEKVYIIAHVPVGYLPSSQNITAMREYYNEKLIDIFQKY
SDVIAGQFYGHTHRDSIMVLSDKKGSPVNSLFVAPAVTPVKSVLEKQTNN
PGIRLFQYDPRDYKLLDMLQYYLNLTEANLKGESIWKLEYILTQTYDIED
LQPESLYGLAKQFTILDSKQFIKYYNYFFVSYDSSVTCDKTCKAFQICAI
MNLDNISYADCLKQL
3D structure
PDB5ebe The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a - an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity.
ChainC
Resolution3.0 Å
3D
structure
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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 C D110 N151 H252 H293 D78 N119 H220 H261
BS02 ZN C D45 H47 D110 H295 D13 H15 D78 H263
BS03 C5P C H47 K66 D110 H152 H293 H295 K323 H15 K34 D78 H120 H261 H263 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

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:5ebe, PDBe:5ebe, PDBj:5ebe
PDBsum5ebe
PubMed26783088
UniProtQ92484|ASM3A_HUMAN Cyclic GMP-AMP phosphodiesterase SMPDL3A (Gene Name=SMPDL3A)

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