Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3VZB

Crystal structure of Sphingosine Kinase 1

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000287	molecular_function	magnesium ion binding
A	0001568	biological_process	blood vessel development
A	0001727	molecular_function	lipid kinase activity
A	0003376	biological_process	sphingosine-1-phosphate receptor signaling pathway
A	0003677	molecular_function	DNA binding
A	0005515	molecular_function	protein binding
A	0005516	molecular_function	calmodulin binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0005905	cellular_component	clathrin-coated pit
A	0005929	cellular_component	cilium
A	0006473	biological_process	protein acetylation
A	0006629	biological_process	lipid metabolic process
A	0006670	biological_process	sphingosine metabolic process
A	0006954	biological_process	inflammatory response
A	0007420	biological_process	brain development
A	0008283	biological_process	cell population proliferation
A	0008284	biological_process	positive regulation of cell population proliferation
A	0008289	molecular_function	lipid binding
A	0008481	molecular_function	sphingosine kinase activity
A	0010008	cellular_component	endosome membrane
A	0010468	biological_process	regulation of gene expression
A	0010803	biological_process	regulation of tumor necrosis factor-mediated signaling pathway
A	0016020	cellular_component	membrane
A	0016301	molecular_function	kinase activity
A	0016407	molecular_function	acetyltransferase activity
A	0016740	molecular_function	transferase activity
A	0017050	molecular_function	obsolete D-erythro-sphingosine kinase activity
A	0019722	biological_process	calcium-mediated signaling
A	0030100	biological_process	regulation of endocytosis
A	0030139	cellular_component	endocytic vesicle
A	0030148	biological_process	sphingolipid biosynthetic process
A	0030307	biological_process	positive regulation of cell growth
A	0030335	biological_process	positive regulation of cell migration
A	0031398	biological_process	positive regulation of protein ubiquitination
A	0031410	cellular_component	cytoplasmic vesicle
A	0031901	cellular_component	early endosome membrane
A	0032651	biological_process	regulation of interleukin-1 beta production
A	0032740	biological_process	positive regulation of interleukin-17 production
A	0034248	biological_process	regulation of amide metabolic process
A	0034612	biological_process	response to tumor necrosis factor
A	0035556	biological_process	intracellular signal transduction
A	0035869	cellular_component	ciliary transition zone
A	0035924	biological_process	cellular response to vascular endothelial growth factor stimulus
A	0038036	molecular_function	sphingosine-1-phosphate receptor activity
A	0043066	biological_process	negative regulation of apoptotic process
A	0045202	cellular_component	synapse
A	0045766	biological_process	positive regulation of angiogenesis
A	0045840	biological_process	positive regulation of mitotic nuclear division
A	0045931	biological_process	positive regulation of mitotic cell cycle
A	0045987	biological_process	positive regulation of smooth muscle contraction
A	0046512	biological_process	sphingosine biosynthetic process
A	0046521	biological_process	sphingoid catabolic process
A	0046890	biological_process	regulation of lipid biosynthetic process
A	0048146	biological_process	positive regulation of fibroblast proliferation
A	0050764	biological_process	regulation of phagocytosis
A	0051049	biological_process	regulation of transport
A	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
A	0051239	biological_process	regulation of multicellular organismal process
A	0051721	molecular_function	protein phosphatase 2A binding
A	0070301	biological_process	cellular response to hydrogen peroxide
A	0071363	biological_process	cellular response to growth factor stimulus
A	0071897	biological_process	DNA biosynthetic process
A	0090520	biological_process	sphingolipid mediated signaling pathway
A	0098793	cellular_component	presynapse
A	0150077	biological_process	regulation of neuroinflammatory response
A	1900060	biological_process	negative regulation of ceramide biosynthetic process
A	1900745	biological_process	positive regulation of p38MAPK cascade
A	1901224	biological_process	positive regulation of non-canonical NF-kappaB signal transduction
A	1903978	biological_process	regulation of microglial cell activation
A	1905364	biological_process	regulation of endosomal vesicle fusion
B	0000166	molecular_function	nucleotide binding
B	0000287	molecular_function	magnesium ion binding
B	0001568	biological_process	blood vessel development
B	0001727	molecular_function	lipid kinase activity
B	0003376	biological_process	sphingosine-1-phosphate receptor signaling pathway
B	0003677	molecular_function	DNA binding
B	0005515	molecular_function	protein binding
B	0005516	molecular_function	calmodulin binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0005905	cellular_component	clathrin-coated pit
B	0005929	cellular_component	cilium
B	0006473	biological_process	protein acetylation
B	0006629	biological_process	lipid metabolic process
B	0006670	biological_process	sphingosine metabolic process
B	0006954	biological_process	inflammatory response
B	0007420	biological_process	brain development
B	0008283	biological_process	cell population proliferation
B	0008284	biological_process	positive regulation of cell population proliferation
B	0008289	molecular_function	lipid binding
B	0008481	molecular_function	sphingosine kinase activity
B	0010008	cellular_component	endosome membrane
B	0010468	biological_process	regulation of gene expression
B	0010803	biological_process	regulation of tumor necrosis factor-mediated signaling pathway
B	0016020	cellular_component	membrane
B	0016301	molecular_function	kinase activity
B	0016407	molecular_function	acetyltransferase activity
B	0016740	molecular_function	transferase activity
B	0017050	molecular_function	obsolete D-erythro-sphingosine kinase activity
B	0019722	biological_process	calcium-mediated signaling
B	0030100	biological_process	regulation of endocytosis
B	0030139	cellular_component	endocytic vesicle
B	0030148	biological_process	sphingolipid biosynthetic process
B	0030307	biological_process	positive regulation of cell growth
B	0030335	biological_process	positive regulation of cell migration
B	0031398	biological_process	positive regulation of protein ubiquitination
B	0031410	cellular_component	cytoplasmic vesicle
B	0031901	cellular_component	early endosome membrane
B	0032651	biological_process	regulation of interleukin-1 beta production
B	0032740	biological_process	positive regulation of interleukin-17 production
B	0034248	biological_process	regulation of amide metabolic process
B	0034612	biological_process	response to tumor necrosis factor
B	0035556	biological_process	intracellular signal transduction
B	0035869	cellular_component	ciliary transition zone
B	0035924	biological_process	cellular response to vascular endothelial growth factor stimulus
B	0038036	molecular_function	sphingosine-1-phosphate receptor activity
B	0043066	biological_process	negative regulation of apoptotic process
B	0045202	cellular_component	synapse
B	0045766	biological_process	positive regulation of angiogenesis
B	0045840	biological_process	positive regulation of mitotic nuclear division
B	0045931	biological_process	positive regulation of mitotic cell cycle
B	0045987	biological_process	positive regulation of smooth muscle contraction
B	0046512	biological_process	sphingosine biosynthetic process
B	0046521	biological_process	sphingoid catabolic process
B	0046890	biological_process	regulation of lipid biosynthetic process
B	0048146	biological_process	positive regulation of fibroblast proliferation
B	0050764	biological_process	regulation of phagocytosis
B	0051049	biological_process	regulation of transport
B	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
B	0051239	biological_process	regulation of multicellular organismal process
B	0051721	molecular_function	protein phosphatase 2A binding
B	0070301	biological_process	cellular response to hydrogen peroxide
B	0071363	biological_process	cellular response to growth factor stimulus
B	0071897	biological_process	DNA biosynthetic process
B	0090520	biological_process	sphingolipid mediated signaling pathway
B	0098793	cellular_component	presynapse
B	0150077	biological_process	regulation of neuroinflammatory response
B	1900060	biological_process	negative regulation of ceramide biosynthetic process
B	1900745	biological_process	positive regulation of p38MAPK cascade
B	1901224	biological_process	positive regulation of non-canonical NF-kappaB signal transduction
B	1903978	biological_process	regulation of microglial cell activation
B	1905364	biological_process	regulation of endosomal vesicle fusion
C	0000166	molecular_function	nucleotide binding
C	0000287	molecular_function	magnesium ion binding
C	0001568	biological_process	blood vessel development
C	0001727	molecular_function	lipid kinase activity
C	0003376	biological_process	sphingosine-1-phosphate receptor signaling pathway
C	0003677	molecular_function	DNA binding
C	0005515	molecular_function	protein binding
C	0005516	molecular_function	calmodulin binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0005905	cellular_component	clathrin-coated pit
C	0005929	cellular_component	cilium
C	0006473	biological_process	protein acetylation
C	0006629	biological_process	lipid metabolic process
C	0006670	biological_process	sphingosine metabolic process
C	0006954	biological_process	inflammatory response
C	0007420	biological_process	brain development
C	0008283	biological_process	cell population proliferation
C	0008284	biological_process	positive regulation of cell population proliferation
C	0008289	molecular_function	lipid binding
C	0008481	molecular_function	sphingosine kinase activity
C	0010008	cellular_component	endosome membrane
C	0010468	biological_process	regulation of gene expression
C	0010803	biological_process	regulation of tumor necrosis factor-mediated signaling pathway
C	0016020	cellular_component	membrane
C	0016301	molecular_function	kinase activity
C	0016407	molecular_function	acetyltransferase activity
C	0016740	molecular_function	transferase activity
C	0017050	molecular_function	obsolete D-erythro-sphingosine kinase activity
C	0019722	biological_process	calcium-mediated signaling
C	0030100	biological_process	regulation of endocytosis
C	0030139	cellular_component	endocytic vesicle
C	0030148	biological_process	sphingolipid biosynthetic process
C	0030307	biological_process	positive regulation of cell growth
C	0030335	biological_process	positive regulation of cell migration
C	0031398	biological_process	positive regulation of protein ubiquitination
C	0031410	cellular_component	cytoplasmic vesicle
C	0031901	cellular_component	early endosome membrane
C	0032651	biological_process	regulation of interleukin-1 beta production
C	0032740	biological_process	positive regulation of interleukin-17 production
C	0034248	biological_process	regulation of amide metabolic process
C	0034612	biological_process	response to tumor necrosis factor
C	0035556	biological_process	intracellular signal transduction
C	0035869	cellular_component	ciliary transition zone
C	0035924	biological_process	cellular response to vascular endothelial growth factor stimulus
C	0038036	molecular_function	sphingosine-1-phosphate receptor activity
C	0043066	biological_process	negative regulation of apoptotic process
C	0045202	cellular_component	synapse
C	0045766	biological_process	positive regulation of angiogenesis
C	0045840	biological_process	positive regulation of mitotic nuclear division
C	0045931	biological_process	positive regulation of mitotic cell cycle
C	0045987	biological_process	positive regulation of smooth muscle contraction
C	0046512	biological_process	sphingosine biosynthetic process
C	0046521	biological_process	sphingoid catabolic process
C	0046890	biological_process	regulation of lipid biosynthetic process
C	0048146	biological_process	positive regulation of fibroblast proliferation
C	0050764	biological_process	regulation of phagocytosis
C	0051049	biological_process	regulation of transport
C	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
C	0051239	biological_process	regulation of multicellular organismal process
C	0051721	molecular_function	protein phosphatase 2A binding
C	0070301	biological_process	cellular response to hydrogen peroxide
C	0071363	biological_process	cellular response to growth factor stimulus
C	0071897	biological_process	DNA biosynthetic process
C	0090520	biological_process	sphingolipid mediated signaling pathway
C	0098793	cellular_component	presynapse
C	0150077	biological_process	regulation of neuroinflammatory response
C	1900060	biological_process	negative regulation of ceramide biosynthetic process
C	1900745	biological_process	positive regulation of p38MAPK cascade
C	1901224	biological_process	positive regulation of non-canonical NF-kappaB signal transduction
C	1903978	biological_process	regulation of microglial cell activation
C	1905364	biological_process	regulation of endosomal vesicle fusion

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SQS A 401

Chain	Residue
A	LEU167
A	SER168
A	ASP178
A	PHE192
A	LEU268
A	MET272
A	HOH680

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 A 402

Chain	Residue
A	LYS27
A	ALA110
A	GLY111
A	SER112
A	ARG185
A	HOH654
A	HOH675
A	GLY25
A	GLY26

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 403

Chain	Residue
A	CYS106
A	SER107
A	LEU108
A	LEU120
A	CYS138
A	MET361
A	VAL362

site_id	AC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 404

Chain	Residue
A	LEU213
A	VAL218
A	GLY219
A	LYS221
A	THR222
A	HIS237
A	HIS248
A	HOH510

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 405

Chain	Residue
A	THR157
A	ALA158
A	SER159
A	LYS335
A	SER347
A	GLU348

site_id	AC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 406

Chain	Residue
A	TRP171
A	GLY172
A	ALA175
A	ASP176
A	TYR206
A	GLY336
A	VAL337
A	HOH525

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 407

Chain	Residue
A	MET150
A	ASN151
A	ARG279
A	CYS280
A	HOH558

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 408

Chain	Residue
A	HIS122
A	TYR123
A	ARG279
A	HOH590

site_id	AC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SQS B 401

Chain	Residue
B	ASP81
B	LEU167
B	SER168
B	ILE174
B	ASP178
B	MET272
B	HOH576

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 402

Chain	Residue
B	GLY26
B	LYS27
B	GLY111
B	SER112
B	ARG191
B	HOH582

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 403

Chain	Residue
B	GLU67
B	GLU68
B	LEU69
B	GLY70
B	ARG94
B	ASP96

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 404

Chain	Residue
B	GLU62
B	LEU63
B	SER66
C	ARG16
C	HOH503

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 405

Chain	Residue
B	ARG16
B	ARG71
B	TRP72
B	HOH513

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 406

Chain	Residue
B	PRO149
B	ARG279
B	CYS280
B	ASN357
B	HOH512
B	HOH545

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 407

Chain	Residue
B	GLY113
B	ASN114
B	GLY269
B	SER270

site_id	BC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 401

Chain	Residue
C	HOH536
C	GLY26
C	LYS27
C	GLY111
C	SER112
C	GLY188
C	GLU189
C	ARG191

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO C 402

Chain	Residue
C	LEU69
C	GLY70
C	THR99
C	ALA100
C	LYS103

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 403

Chain	Residue
C	VAL294
C	SER295
C	MET298
C	CYS316
C	PRO317
C	TYR318

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO C 404

Chain	Residue
C	MET150
C	ASN151
C	HIS265
C	ARG279
C	CYS280

site_id	CC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO C 405

Chain	Residue
C	ARG296
C	ALA297

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	441
Details	Domain: {"description":"DAGKc","evidences":[{"source":"PROSITE-ProRule","id":"PRU00783","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	24
Details	Motif: {"description":"Nuclear export signal 1","evidences":[{"source":"PubMed","id":"14575709","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	24
Details	Motif: {"description":"Nuclear export signal 2","evidences":[{"source":"PubMed","id":"14575709","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	3
Details	Active site: {"description":"Proton donor/acceptor","evidences":[{"source":"PubMed","id":"23602659","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	51
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23602659","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	3
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"20577214","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)