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- PDB-3vzc: Crystal structure of Sphingosine Kinase 1 with inhibitor -

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Basic information

Entry
Database: PDB / ID: 3vzc
TitleCrystal structure of Sphingosine Kinase 1 with inhibitor
ComponentsSphingosine kinase 1
KeywordsTRANSFERASE/INHIBITOR / lipid kinase / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


sphingosine kinase / sphinganine kinase activity / D-erythro-sphingosine kinase activity / sphingoid catabolic process / regulation of endosomal vesicle fusion / sphingosine metabolic process / negative regulation of ceramide biosynthetic process / sphingosine-1-phosphate receptor activity / regulation of microglial cell activation / regulation of interleukin-1 beta production ...sphingosine kinase / sphinganine kinase activity / D-erythro-sphingosine kinase activity / sphingoid catabolic process / regulation of endosomal vesicle fusion / sphingosine metabolic process / 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 / protein phosphatase 2A binding / positive regulation of peptidyl-threonine phosphorylation / VEGFR2 mediated cell proliferation / positive regulation of protein ubiquitination / calcium-mediated signaling / brain development / PKR-mediated signaling / 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 / cytosol / cytoplasm
Similarity search - Function
Tumour Suppressor Smad4 - #40 / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) / Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Tumour Suppressor Smad4 / Sandwich ...Tumour Suppressor Smad4 - #40 / Diacylglycerol kinase, catalytic domain / Diacylglycerol kinase catalytic domain / DAG-kinase catalytic (DAGKc) domain profile. / Diacylglycerol kinase catalytic domain (presumed) / Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Tumour Suppressor Smad4 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-UUL / Sphingosine kinase 1
Similarity search - Component
Biological specieshomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsMin, X. / Walker, N.P. / Wang, Z.
CitationJournal: Structure / Year: 2013
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
DepositionOct 11, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sphingosine kinase 1
B: Sphingosine kinase 1
C: Sphingosine kinase 1
D: Sphingosine kinase 1
E: Sphingosine kinase 1
F: Sphingosine kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,44614
Polymers239,5056
Non-polymers1,9418
Water5,260292
1
A: Sphingosine kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2202
Polymers39,9171
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sphingosine kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2202
Polymers39,9171
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sphingosine kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2202
Polymers39,9171
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sphingosine kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2823
Polymers39,9171
Non-polymers3652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Sphingosine kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2202
Polymers39,9171
Non-polymers3031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Sphingosine kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2823
Polymers39,9171
Non-polymers3652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.220, 106.610, 226.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Sphingosine kinase 1 / / SK 1 / SPK 1


Mass: 39917.469 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 9-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) homo sapiens (human) / Cell line: sf9 / Gene: SPHK1, SPHK, SPK / Plasmid: pFastBac HTb / References: UniProt: Q9NYA1, sphingosine kinase
#2: Chemical
ChemComp-UUL / 4-{[4-(4-chlorophenyl)-1,3-thiazol-2-yl]amino}phenol


Mass: 302.779 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H11ClN2OS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.16 % / Mosaicity: 0.34 °
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC315R / Detector: CCD / Details: 3x3 CCD array
RadiationMonochromator: Double-crystal, Si(111) / Protocol: MAD / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.423.30.450.3811.945115136350.2370.450.3813.185.6
2.42-2.573.30.3130.2652.842469128850.1650.3130.2654.485.7
2.57-2.753.30.2130.184.140430123940.1120.2130.18687.2
2.75-2.973.20.1380.1166.338615119040.0730.1380.1168.790.1
2.97-3.253.20.0940.0798.637112115350.050.0940.07912.494.6
3.25-3.643.30.0610.05211.735548108000.0320.0610.05217.797.5
3.64-4.23.40.0490.04113.53370197760.0260.0490.04121.999.5
4.2-5.143.60.0490.04212.33021583770.0250.0490.04225.299.9
5.14-7.273.60.0530.04510.72364465120.0270.0530.04522.999.5
7.27-49.9543.90.0350.0315.21454037430.0180.0350.0325.798.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2877 / WRfactor Rwork: 0.2323 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7464 / SU B: 8.889 / SU ML: 0.213 / SU R Cruickshank DPI: 0.4048 / SU Rfree: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.405 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2846 5084 5 %RANDOM
Rwork0.229 ---
obs0.2318 101479 91.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.7 Å2 / Biso mean: 44.2649 Å2 / Biso min: 16.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.14 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16048 0 128 292 16468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01916556
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.98622449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75652045
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94522.185691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.596152731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.49215150
X-RAY DIFFRACTIONr_chiral_restr0.0970.22511
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112486
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 334 -
Rwork0.306 6199 -
all-6533 -
obs--84.89 %

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