+
Open data
-
Basic information
Entry | Database: PDB / ID: 3vzc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Sphingosine Kinase 1 with inhibitor | ||||||
![]() | Sphingosine kinase 1 | ||||||
![]() | TRANSFERASE/INHIBITOR / lipid kinase / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | ![]() sphingosine kinase / sphinganine kinase activity / D-erythro-sphingosine kinase activity / sphingoid catabolic process / regulation of endosomal vesicle fusion / sphingosine metabolic process / lipid kinase activity / negative regulation of ceramide biosynthetic process / sphingosine-1-phosphate receptor activity / regulation of microglial cell activation ...sphingosine kinase / sphinganine kinase activity / D-erythro-sphingosine kinase activity / sphingoid catabolic process / regulation of endosomal vesicle fusion / sphingosine metabolic process / lipid kinase activity / negative regulation of ceramide biosynthetic process / sphingosine-1-phosphate receptor activity / regulation of microglial cell activation / regulation of interleukin-1 beta production / sphingosine biosynthetic process / sphingolipid biosynthetic process / regulation of neuroinflammatory response / Sphingolipid de novo biosynthesis / positive regulation of smooth muscle contraction / regulation of phagocytosis / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of p38MAPK cascade / DNA biosynthetic process / protein acetylation / blood vessel development / positive regulation of interleukin-17 production / Association of TriC/CCT with target proteins during biosynthesis / acetyltransferase activity / regulation of endocytosis / endocytic vesicle / cellular response to vascular endothelial growth factor stimulus / response to tumor necrosis factor / clathrin-coated pit / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of mitotic cell cycle / positive regulation of mitotic nuclear division / positive regulation of peptidyl-threonine phosphorylation / VEGFR2 mediated cell proliferation / protein phosphatase 2A binding / positive regulation of protein ubiquitination / calcium-mediated signaling / PKR-mediated signaling / brain development / cellular response to growth factor stimulus / cellular response to hydrogen peroxide / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of angiogenesis / positive regulation of fibroblast proliferation / presynapse / positive regulation of NF-kappaB transcription factor activity / early endosome membrane / positive regulation of cell growth / cell population proliferation / Extra-nuclear estrogen signaling / calmodulin binding / intracellular signal transduction / positive regulation of cell migration / inflammatory response / phosphorylation / intracellular membrane-bounded organelle / lipid binding / negative regulation of apoptotic process / magnesium ion binding / DNA binding / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Min, X. / Walker, N.P. / Wang, Z. | ||||||
![]() | ![]() Title: Molecular basis of sphingosine kinase 1 substrate recognition and catalysis. Authors: Wang, Z. / Min, X. / Xiao, S.H. / Johnstone, S. / Romanow, W. / Meininger, D. / Xu, H. / Liu, J. / Dai, J. / An, S. / Thibault, S. / Walker, N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 407.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 333.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 78.5 KB | Display | |
Data in CIF | ![]() | 105.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
5 | ![]()
| ||||||||
6 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 39917.469 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 9-364 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #2: Chemical | ChemComp-UUL / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.16 % / Mosaicity: 0.34 ° |
---|---|
Crystal grow | Temperature: 289 K / Method: sitting drop / pH: 6 Details: 1.0-1.4M ammonium sulfate, 0.3-1.3M NaCl, 0.1M Bis-Tris, pH 6.0, sitting drop, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC315R / Detector: CCD / Details: 3x3 CCD array | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: MAD / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→113.09 Å / Num. all: 101561 / Num. obs: 101561 / % possible obs: 92.1 % / Redundancy: 3.4 % / Rsym value: 0.057 / Net I/σ(I): 12.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.7 Å2 / Biso mean: 44.2649 Å2 / Biso min: 16.49 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
|