› 2x6k

X-ray diffraction
3.5Å resolution

THE CRYSTAL STRUCTURE OF THE DROSOPHILA CLASS III PI3-KINASE VPS34 IN COMPLEX WITH PI-103

Released:
DOI: 10.2210/pdb2x6k/pdb
PDB entry 2x6k coloured by chain, front view.
PDB entry 2x6k coloured by chain, side view.
PDB entry 2x6k coloured by chain, top view.
Source organism: Drosophila melanogaster
Primary publication:
Shaping development of autophagy inhibitors with the structure of the lipid kinase Vps34.
Miller S, Tavshanjian B, Oleksy A, Perisic O, Houseman BT, Shokat KM, Williams RL
Science 327 1638-42 (2010)
PMID: 20339072

Function and Biology Details

Reaction catalysed: 
ATP + 1-phosphatidyl-1D-myo-inositol = ADP + 1-phosphatidyl-1D-myo-inositol 3-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194334 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphatidylinositol 3-kinase catalytic subunit type 3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 696 amino acids
Theoretical weight: 78.77 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9W1M7 (Residues: 258-949; Coverage: 73%)
Gene names: CG5373, DmVps34, Dmel\CG5373, Dmel_CG5373, PI(3)K, PI3K, PI3K-59F, PI3K59F, PI3K_59F, PIK359F, PI[[3]]K, Pi3K59F, Pi3K_59F, Pi3k59F, VPS34, Vps34, dPI3K, dVps34, vps34
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand SO4 3 x SO4
Ligand X6K 2 x X6K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: I212121
Unit cell:
a: 111.44Å b: 155.68Å c: 244Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.235 0.296
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

45 review citations

Eaten alive: a history of macroautophagy.
Yang et al. (2010)
44 more

2 mentions without citation

Shaping development of autophagy inhibitors with the structure of the lipid kinase Vps34.
Miller et al. (2010)
1 more