Structure of PDB 5ebe Chain B Binding Site BS01

Receptor Information
>5ebe Chain B (length=415) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PPPAIGQFWHVTDLHLDPTYHITDDHTKVCASSKGANASNPGPFGDVLCD
SPYQLILSAFDFIKNSGQEASFMIWTGDSPPHVPVPELSTDTVINVITNM
TTTIQSLFPNLQVFPALGNHDYWPQDQLPVVTSKVYNAVANLWKPWLDEE
AISTLRKGGFYSQKVTTNPNLRIISLNTNLYYGPNIMTLNKTDPANQFEW
LESTLNNSQQNKEKVYIIAHVPVGYLPSSQNITAMREYYNEKLIDIFQKY
SDVIAGQFYGHTHRDSIMVLSDKKGSPVNSLFVAPAVTPVKSVLEKQTNN
PGIRLFQYDPRDYKLLDMLQYYLNLTEANLKGESIWKLEYILTQTYDIED
LQPESLYGLAKQFTILDSKQFIKYYNYFFVSYDSSVTCDKTCKAFQICAI
MNLDNISYADCLKQL
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain5ebe Chain B Residue 606 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ebe The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a - an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		D45 H47 D110 H295
Binding residue
(residue number reindexed from 1)		D13 H15 D78 H263
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.4.-
3.6.1.15: nucleoside-triphosphate phosphatase.
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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