Structure of PDB 5kar Chain A Binding Site BS02

Receptor Information
>5kar Chain A (length=412) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LGRFWHISDLHLDPNYTVSKDPLQVCPSAGSQPVLNAGPWGDYLCDSPWA
LINSSLYAMKEIEPKPDFILWTGDDTPHVPNESLGEAAVLAIVERLTNLI
KEVFPDTKVYAALGNHDFHPKNQFPAQSNRIYNQVAELWRPWLSNESYAL
FKRGAFYSEKLPGPSRAGRVVVLNTNLYYSNNEQTAGMADPGEQFRWLGD
VLSNASRDGEMVYVIGHVPPGFFEKTQNKAWFRESFNEEYLKVIQKHHRV
IAGQFFGHHHTDSFRMFYDNTGAPINVMFLTPGVTPWKTTLPGVVDGANN
PGIRIFEYDRATLNLKDLVTYFLNLRQANVQETPRWEQEYRLTEAYQVPD
ASVSSMHTALTRIASEPHILQRYYVYNSVSYNHLTCEDSCRIEHVCAIQH
VAFNTYATCLHG
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 chain5kar Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5kar Crystal Structure of the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3B Provides Insights into Determinants of Substrate Specificity.
Resolution1.142 Å
Binding residue
(original residue number in PDB)		D28 H30 D93 H279
Binding residue
(residue number reindexed from 1)		D9 H11 D74 H260
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.4.-
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:0016798 hydrolase activity, acting on glycosyl bonds
GO:0046872 metal ion binding
Biological Process
GO:0006685 sphingomyelin catabolic process
GO:0006954 inflammatory response
GO:0016042 lipid catabolic process
GO:0034122 negative regulation of toll-like receptor signaling pathway
GO:0045087 innate immune response
GO:0045824 negative regulation of innate immune response
GO:0046466 membrane lipid catabolic process
GO:0050728 negative regulation of inflammatory response
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005886 plasma membrane
GO:0098552 side of membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5kar, PDBe:5kar, PDBj:5kar
PDBsum5kar
PubMed27687724
UniProtP58242|ASM3B_MOUSE Acid sphingomyelinase-like phosphodiesterase 3b (Gene Name=Smpdl3b)

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