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- PDB-3vzd: Crystal structure of Sphingosine Kinase 1 with inhibitor and ADP -

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Basic information

Entry
Database: PDB / ID: 3vzd
TitleCrystal structure of Sphingosine Kinase 1 with inhibitor and ADP
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 / lipid kinase activity / sphingosine-1-phosphate receptor activity / negative regulation of ceramide biosynthetic process / 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 / lipid kinase activity / sphingosine-1-phosphate receptor activity / negative regulation of ceramide biosynthetic process / regulation of interleukin-1 beta production / regulation of microglial cell activation / 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 / Association of TriC/CCT with target proteins during biosynthesis / acetyltransferase activity / positive regulation of interleukin-17 production / 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 nuclear division / positive regulation of mitotic cell cycle / phosphorylation / VEGFR2 mediated cell proliferation / positive regulation of peptidyl-threonine phosphorylation / protein phosphatase 2A binding / 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 / 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 ...: / 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
ADENOSINE-5'-DIPHOSPHATE / PYROPHOSPHATE 2- / 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 1, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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)242,83422
Polymers239,5056
Non-polymers3,32916
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sphingosine kinase 1
hetero molecules

D: Sphingosine kinase 1
hetero molecules

B: Sphingosine kinase 1
C: Sphingosine kinase 1
hetero molecules

E: Sphingosine kinase 1
F: Sphingosine kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,83422
Polymers239,5056
Non-polymers3,32916
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
crystal symmetry operation4_535x+1/2,-y-3/2,-z1
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area13170 Å2
ΔGint-112 kcal/mol
Surface area75170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.202, 106.573, 226.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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

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Non-polymers , 6 types, 374 molecules

#2: Chemical
ChemComp-UUL / 4-{[4-(4-chlorophenyl)-1,3-thiazol-2-yl]amino}phenol


Mass: 302.779 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C15H11ClN2OS
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 52.13 %
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→113.228 Å / Num. all: 108742 / Num. obs: 108742 / % possible obs: 98.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 14.3
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
2.3-2.423.50.4320.368254012154550.2230.4320.3683.197.3
2.42-2.573.50.3120.2662.752151147610.1610.3120.2664.398.2
2.57-2.753.60.2240.1913.749841139950.1160.2240.1916.198.6
2.75-2.973.60.1470.1255.747342130820.0760.1470.1259.399
2.97-3.253.60.0940.0818.344121121100.0490.0940.08114.499.4
3.25-3.643.70.0650.05510.840525110200.0330.0650.05521.299.5
3.64-4.23.70.0550.04711.53561597500.0290.0550.04726.699.4
4.2-5.143.50.0460.03913.42927783320.0240.0460.03930.599.6
5.14-7.273.50.0490.04212.62253864650.0260.0490.04228.998.9
7.27-96.3953.50.0390.03312.71336837720.020.0390.03332.999.6

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.2023 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7898 / SU B: 7.645 / SU ML: 0.185 / SU R Cruickshank DPI: 0.3294 / SU Rfree: 0.2546 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 5435 5 %RANDOM
Rwork0.2055 ---
obs0.2086 108661 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 158.33 Å2 / Biso mean: 38.7938 Å2 / Biso min: 12.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2---0.99 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16208 0 209 358 16775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02216808
X-RAY DIFFRACTIONr_angle_refined_deg2.041.99322803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.45952064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54922.045709
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.358152783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.32215162
X-RAY DIFFRACTIONr_chiral_restr0.1480.22531
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112691
X-RAY DIFFRACTIONr_mcbond_it1.0991.510310
X-RAY DIFFRACTIONr_mcangle_it2.024216511
X-RAY DIFFRACTIONr_scbond_it2.99836498
X-RAY DIFFRACTIONr_scangle_it4.744.56292
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 360 -
Rwork0.251 7423 -
all-7783 -
obs--96.91 %

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