Structure of PDB 3vzd Chain B

Receptor sequence

>3vzdB (length=342) Species: 9606 (Homo sapiens) [Search protein sequence]

GVLPRPCRVLVLLNPRGGKGKALQLFRSHVQPLLAEAEISFTLMLTERRN
HARELVRSEELGRWDALVVMSGDGLMHEVVNGLMERPDWETAIQKPLCSL
PAGSGNALAASLNHYAGYEQVTNEDLLTNCTLLLCRRLLSPMNLLSLHTA
SGLRLFSVLSLAWGFIADVDLESEKYRRLGEMRFTLGTFLRLAALRTYRG
RLAYLPVGRGPVDAHLVPLEEPVPSHWTVVPDEDFVLVLALLHSHLGSEM
FAAPMGRCAAGVMHLFYVRAGVSRAMLLRLFLAMEKGRHMEYECPYLVYV
PVVAFRLEPKDGKGVFAVDGELMVSEAVQGQVHPNYFWMVSG

3D structure

PDB

3vzd Molecular basis of sphingosine kinase 1 substrate recognition and catalysis.

Chain

Resolution

2.3 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

2.3.1.-
2.7.1.91: sphingosine kinase.

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	UUL	B	F173 I174 V177 D178 T196 L259 M272 F288 F303 H311	F165 I166 V169 D170 T188 L237 M250 F266 F281 H289	BindingDB: Ki=16000nM,IC50=35000nM
BS02	POP	B	S79 G80 G82 L83 G111 S112 G113	S71 G72 G74 L75 G103 S104 G105
BS03	MG	B	G82 G342 E343	G74 G320 E321

Gene Ontology

	Molecular Function
GO:0000287	magnesium ion binding
GO:0001727	lipid kinase activity
GO:0003677	DNA binding
GO:0005515	protein binding
GO:0005516	calmodulin binding
GO:0005524	ATP binding
GO:0008289	lipid binding
GO:0008481	sphingosine kinase activity
GO:0016301	kinase activity
GO:0016407	acetyltransferase activity
GO:0017050	D-erythro-sphingosine kinase activity
GO:0038036	sphingosine-1-phosphate receptor activity
GO:0051721	protein phosphatase 2A binding

	Biological Process
GO:0001568	blood vessel development
GO:0003376	sphingosine-1-phosphate receptor signaling pathway
GO:0006473	protein acetylation
GO:0006629	lipid metabolic process
GO:0006670	sphingosine metabolic process
GO:0006954	inflammatory response
GO:0007420	brain development
GO:0008283	cell population proliferation
GO:0008284	positive regulation of cell population proliferation
GO:0010800	positive regulation of peptidyl-threonine phosphorylation
GO:0010803	regulation of tumor necrosis factor-mediated signaling pathway
GO:0016310	phosphorylation
GO:0019722	calcium-mediated signaling
GO:0030100	regulation of endocytosis
GO:0030148	sphingolipid biosynthetic process
GO:0030307	positive regulation of cell growth
GO:0030335	positive regulation of cell migration
GO:0031398	positive regulation of protein ubiquitination
GO:0032651	regulation of interleukin-1 beta production
GO:0032740	positive regulation of interleukin-17 production
GO:0034612	response to tumor necrosis factor
GO:0035556	intracellular signal transduction
GO:0035924	cellular response to vascular endothelial growth factor stimulus
GO:0043066	negative regulation of apoptotic process
GO:0045766	positive regulation of angiogenesis
GO:0045840	positive regulation of mitotic nuclear division
GO:0045931	positive regulation of mitotic cell cycle
GO:0045987	positive regulation of smooth muscle contraction
GO:0046512	sphingosine biosynthetic process
GO:0046521	sphingoid catabolic process
GO:0048146	positive regulation of fibroblast proliferation
GO:0050764	regulation of phagocytosis
GO:0051092	positive regulation of NF-kappaB transcription factor activity
GO:0070301	cellular response to hydrogen peroxide
GO:0071363	cellular response to growth factor stimulus
GO:0071897	DNA biosynthetic process
GO:0090520	sphingolipid mediated signaling pathway
GO:0150077	regulation of neuroinflammatory response
GO:1900060	negative regulation of ceramide biosynthetic process
GO:1900745	positive regulation of p38MAPK cascade
GO:1901224	positive regulation of non-canonical NF-kappaB signal transduction
GO:1903978	regulation of microglial cell activation
GO:1905364	regulation of endosomal vesicle fusion

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005768	endosome
GO:0005829	cytosol
GO:0005886	plasma membrane
GO:0005905	clathrin-coated pit
GO:0010008	endosome membrane
GO:0016020	membrane
GO:0030139	endocytic vesicle
GO:0031901	early endosome membrane
GO:0043231	intracellular membrane-bounded organelle
GO:0045202	synapse
GO:0098793	presynapse

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:3vzd, PDBe:3vzd, PDBj:3vzd
PDBsum	3vzd
PubMed	23602659
UniProt	Q9NYA1\|SPHK1_HUMAN Sphingosine kinase 1 (Gene Name=SPHK1)

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