Structure of PDB 5fca Chain B

Receptor sequence

>5fcaB (length=426) Species: 10090 (Mus musculus)

HKLVPLAPADRAPAVGQFWHVTDLHLDPTYHITDDRTKVCASSKGANASN
PGPFGDVLCDSPYQLILSAFDFIKNSGQEASFMIWTGDSPPHVPVPELST
GTVIKVITNMTMTVQNLFPNLQVFPALGNHDYWPQDQLPIVTSKVYSAVA
DLWKPWLGEEAISTLKKGGFYSQKVASNPGLRIISLNTNLYYGPNIMTLN
KTDPANQFEWLENTLNSSLWNKEKVYIIAHVPVGYLPYATDTPAIRQYYN
EKLLDIFRRYSSVIAGQFYGHTHRDSLMVLSDKNGNPLNSVFVAPAVTPV
KGVLQKETNNPGVRLFQYKPGDYTLLDMVQYYLNLTEANLKGESNWTLEY
VLTQAYSVADLQPKSLYALVQQFATKDSKQFLKYYHYYFVSYDSSATCDQ
HCKTLQVCAIMNLDSMSYDDCLKQHL

3D structure

• PDB: 5fca Structural Basis for Nucleotide Hydrolysis by the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3A.
• Chain: B
• Resolution: 1.924 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	B	D260 D438	D241 D419
BS02	ZN	B	D42 H44 D107 H292	D23 H25 D88 H273
BS03	ZN	B	D107 N148 H249 H290	D88 N129 H230 H271
BS04	ZN	B	H111 H149	H92 H130

Gene Ontology

Molecular Function

• GO:0004767 sphingomyelin phosphodiesterase activity
• 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:0008150 biological_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

External links

• PDB: RCSB:5fca, PDBe:5fca, PDBj:5fca
• PDBsum: 5fca
• PubMed: 26792860
• UniProt: P70158|ASM3A_MOUSE Cyclic GMP-AMP phosphodiesterase SMPDL3A (Gene Name=Smpdl3a)