Structure of PDB 5jg8 Chain B Binding Site BS01

Receptor Information
>5jg8 Chain B (length=530) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FGWGNLTCPICKGLFTAINLGLKKEPNVARVGSVAIKLCNLLKIAPPAVC
QSIVHLFEDDMVEVWRRSVLSPSEACGLLLGSTCGHWDIFSSWNISLPTV
PKPPPKPPSPPAPGAPVSRILFLTDLHWDHDYLEGTDPDCADPLCCRRGS
GLPPASRPGAGYWGEYSKCDLPLRTLESLLSGLGPAGPFDMVYWTGDIPA
HDVWHQTRQDQLRALTTVTALVRKFLGPVPVYPAVGNHESTPVNSFPPPF
IEGNHSSRWLYEAMAKAWEPWLPAEALRTLRIGGFYALSPYPGLRLISLN
MNFCSRENFWLLINSTDPAGQLQWLVGELQAAEDRGDKVHIIGHIPPGHC
LKSWSWNYYRIVARYENTLAAQFFGHTHVDEFEVFYDEETLSRPLAVAFL
APSATTYIGLNPGYRVYQIDGNYSGSSHVVLDHETYILNLTQANIPGAIP
HWQLLYRARETYGLPNTLPTAWHNLVYRMRGDMQLFQTFWFLYHKGHPPS
EPCGTPCRLATLCAQLSARADSPALCRHLM
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 chain5jg8 Chain B Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5jg8 Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		D206 H208 D278 H459
Binding residue
(residue number reindexed from 1)		D125 H127 D197 H378
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.4.12: sphingomyelin phosphodiesterase.
3.1.4.3: phospholipase C.
Gene Ontology
Molecular Function
GO:0004767 sphingomyelin phosphodiesterase activity
GO:0005515 protein binding
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:0006684 sphingomyelin metabolic process
GO:0006685 sphingomyelin catabolic process
GO:0007165 signal transduction
GO:0007399 nervous system development
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:0046479 glycosphingolipid catabolic process
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
GO:0043202 lysosomal lumen
GO:0070062 extracellular exosome

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5jg8, PDBe:5jg8, PDBj:5jg8
PDBsum5jg8
PubMed27349982
UniProtP17405|ASM_HUMAN Sphingomyelin phosphodiesterase (Gene Name=SMPD1)

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