Structure of PDB 5fib Chain B

Receptor sequence
>5fibB (length=534) Species: 10090 (Mus musculus) [Search protein sequence]
HHHHHHKLNLTCPACKVLFTALNHGLKKEPNVARVGSVAIKICKMLNIAP
LDVCQSAVHLFEDDVVEVWTRSVLSPSEACGLLLGSSCGHWDIFSTWNIS
LPSVPKPPPKPPSPPAPGAPVSRVLFLTDLHWDHEYLEGTDPYCADPLCC
RRGSGWPPNSQKGAGFWGEYSKCDLPLRTLESLLKGLGPAGPFEMVYWTG
DIPAHDVWQQSRQDQLRALTTITDLVRKFLGPVPVYPAVGNHESTPVNGF
PPPFIKGNQSSQWLYEAMAKAWEPWLPADALHTLRIGGFYALTPRPGLRL
ISLNMNFCSRENFWLLINSTDPAGQLQWLVEELQAAENRGDKVHIIGHIP
PGHCLKSWSWNYYKIIARYENTLAGQFFGHTHVDEFEIFYDEETLSRPLA
VAFLAPSATTFINLNPGYRVYQIDGNYPGSSHVVLDHETYILNLTQANAA
GGTPSWKRLYRARETYGLPDAMPASWHNLVYRMRDDEQLFQTFWFLYHKG
HPPSEPCGTPCRLATLCAQLSARADSPALCRHLM
3D structure
PDB5fib Crystal structure of mammalian acid sphingomyelinase.
ChainB
Resolution2.8 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Enzyme Commision number 3.1.4.12: sphingomyelin phosphodiesterase.
3.1.4.3: phospholipase C.
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 MAN B K91 S152 K16 S77
BS02 ZN B D204 H206 D276 H457 D129 H131 D201 H382
BS03 ZN B D276 N316 H423 H455 D201 N241 H348 H380
BS04 ZN B H78 H80 H3 H5
Gene Ontology
Molecular Function
GO:0004767 sphingomyelin phosphodiesterase activity
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0034480 phosphatidylcholine phospholipase C activity
GO:0046872 metal ion binding
GO:0061750 acid sphingomyelin phosphodiesterase activity
Biological Process
GO:0001778 plasma membrane repair
GO:0006629 lipid metabolic process
GO:0006672 ceramide metabolic process
GO:0006685 sphingomyelin catabolic process
GO:0008203 cholesterol metabolic process
GO:0009410 response to xenobiotic stimulus
GO:0009615 response to virus
GO:0010212 response to ionizing radiation
GO:0023021 termination of signal transduction
GO:0034340 response to type I interferon
GO:0034612 response to tumor necrosis factor
GO:0034644 cellular response to UV
GO:0042060 wound healing
GO:0042220 response to cocaine
GO:0043065 positive regulation of apoptotic process
GO:0043407 negative regulation of MAP kinase activity
GO:0045807 positive regulation of endocytosis
GO:0046513 ceramide biosynthetic process
GO:0046598 positive regulation of viral entry into host cell
GO:0046718 symbiont entry into host cell
GO:0070555 response to interleukin-1
GO:0071277 cellular response to calcium ion
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005764 lysosome
GO:0005768 endosome
GO:0005811 lipid droplet
GO:0005886 plasma membrane
GO:0036019 endolysosome
GO:0042599 lamellar body

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5fib, PDBe:5fib, PDBj:5fib
PDBsum5fib
PubMed27435900
UniProtQ04519|ASM_MOUSE Sphingomyelin phosphodiesterase (Gene Name=Smpd1)

[Back to BioLiP]