Structure of PDB 3vzd Chain A

Receptor sequence
>3vzdA (length=349) Species: 9606 (Homo sapiens) [Search protein sequence]
MGSGVLPRPCRVLVLLNPRGGKGKALQLFRSHVQPLLAEAEISFTLMLTE
RRNHARELVRSEELGRWDALVVMSGDGLMHEVVNGLMERPDWETAIQKPL
CSLPAGSGNALAASLNHYAGYEQVTNEDLLTNCTLLLCRRLLSPMNLLSL
HTASGLRLFSVLSLAWGFIADVDLESEKYRRLGEMRFTLGTFLRLAALRT
YRGRLAYLPVGRVGSQGPVDAHLVPLEEPVPSHWTVVPDEDFVLVLALLH
SHLGSEMFAAPMGRCAAGVMHLFYVRAGVSRAMLLRLFLAMEKGRHMEYE
CPYLVYVPVVAFRLEPKDGKGVFAVDGELMVSEAVQGQVHPNYFWMVSG
3D structure
PDB3vzd Molecular basis of sphingosine kinase 1 substrate recognition and catalysis.
ChainA
Resolution2.3 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 A F173 I174 V177 D178 T196 M272 F288 F303 M306 H311 F168 I169 V172 D173 T191 M257 F273 F288 M291 H296 PDBbind-CN: -logKd/Ki=6.30,IC50~0.5uM
BindingDB: Ki=16000nM,IC50=35000nM
BS02 UUL A F197 L200 A201 R296 A297 F192 L195 A196 R281 A282 PDBbind-CN: -logKd/Ki=6.30,IC50~0.5uM
BindingDB: Ki=16000nM,IC50=35000nM
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
PDBsum3vzd
PubMed23602659
UniProtQ9NYA1|SPHK1_HUMAN Sphingosine kinase 1 (Gene Name=SPHK1)

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