› 4v24

X-ray diffraction
1.8Å resolution

Sphingosine kinase 1 in complex with PF-543

Released:
DOI: 10.2210/pdb4v24/pdb
PDB entry 4v24 coloured by chain, front view.
PDB entry 4v24 coloured by chain, side view.
PDB entry 4v24 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal Structure of Sphingosine Kinase 1 with PF-543.
Wang J, Knapp S, Pyne NJ, Pyne S, Elkins JM
ACS Med Chem Lett 5 1329-33 (2014)
PMID: 25516793

Function and Biology Details

Reaction catalysed: 
ATP + a sphingoid base = ADP + a sphingoid base 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192699 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sphingosine kinase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 371 amino acids
Theoretical weight: 41.17 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9NYA1 (Residues: 1-363; Coverage: 95%)
Gene names: SK1, SPHK, SPHK1, SPK
Sequence domains: Diacylglycerol kinase catalytic domain
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand GYR 2 x GYR
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21
Unit cell:
a: 86.57Å b: 60.549Å c: 89.592Å
α: 90° β: 107.17° γ: 90°
R-values:
R R work R free
0.183 0.182 0.21
Expression system: Spodoptera frugiperda

Quick links

Citations

13 review citations

Sphingolipid metabolism in cancer signalling and therapy.
Ogretmen B. (2018)
12 more

15 mentions without citation

Sphingolipid biosynthesis in man and microbes.
Harrison et al. (2018)
14 more