› 3vzd

X-ray diffraction
2.3Å resolution

Crystal structure of Sphingosine Kinase 1 with inhibitor and ADP

Released:
DOI: 10.2210/pdb3vzd/pdb
PDB entry 3vzd coloured by chain, front view.
PDB entry 3vzd coloured by chain, side view.
PDB entry 3vzd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis of sphingosine kinase 1 substrate recognition and catalysis.
Wang Z, Min X, Xiao SH, Johnstone S, Romanow W, Meininger D, Xu H, Liu J, Dai J, An S, Thibault S, Walker N
Structure 21 798-809 (2013)
PMID: 23602659

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:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-576426 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sphingosine kinase 1 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 361 amino acids
Theoretical weight: 39.92 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q9NYA1 (Residues: 9-364; Coverage: 93%)
Gene names: SK1, SPHK, SPHK1, SPK
Sequence domains: Diacylglycerol kinase catalytic domain
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand UUL 7 x UUL
Ligand POP 1 x POP
Ligand MG 3 x MG
Ligand CL 3 x CL
Ligand ADP 2 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P212121
Unit cell:
a: 102.202Å b: 106.573Å c: 226.02Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.206 0.269
Expression system: Not provided

Quick links

Citations

30 review citations

Sphingolipids and their metabolism in physiology and disease.
Hannun et al. (2018)
29 more

14 mentions without citation

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