5dfz

X-ray diffraction
4.4Å resolution

Function and Biology Details

Reactions catalysed:
ATP + 1-phosphatidyl-1D-myo-inositol = ADP + 1-phosphatidyl-1D-myo-inositol 3-phosphate
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
Non-polymer only hexamer (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
Vacuolar protein sorting-associated protein 38 Chain: A
Molecule details ›
Chain: A
Length: 441 amino acids
Theoretical weight: 51.07 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q05919 (Residues: 1-439; Coverage: 100%)
Gene names: L8039.11, VPL17, VPS38, YLR360W
Sequence domains: Vacuolar protein sorting 38
Phosphatidylinositol 3-kinase VPS34 Chain: C
Molecule details ›
Chain: C
Length: 875 amino acids
Theoretical weight: 100.97 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22543 (Residues: 1-875; Coverage: 100%)
Gene names: END12, L9672.10, PEP15, VPL7, VPS34, VPT29, YLR240W
Sequence domains:
Serine/threonine-protein kinase VPS15 Chain: B
Molecule details ›
Chain: B
Length: 1460 amino acids
Theoretical weight: 167.08 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22219 (Residues: 1-1454; Coverage: 99%)
Gene names: GRD8, VAC4, VPL19, VPS15, YBR0825, YBR097W
Sequence domains: Protein kinase domain
Nanobody binding S. cerevisiae Vps34 Chain: E
Molecule details ›
Chain: E
Length: 124 amino acids
Theoretical weight: 13.77 KDa
Source organism: Lama glama
Expression system: Escherichia coli
Vacuolar protein sorting-associated protein 30 Chain: D
Molecule details ›
Chain: D
Length: 559 amino acids
Theoretical weight: 63.4 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02948 (Residues: 1-557; Coverage: 100%)
Gene names: APG6, ATG6, LPH7, VPS30, VPT30, YPL120W
Sequence domains:
Putative N-terminal domain of S. cerevisiae Vps30 Chain: G
Molecule details ›
Chain: G
Length: 49 amino acids
Theoretical weight: 4.19 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21212
Unit cell:
a: 215.18Å b: 226.84Å c: 127.21Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.369 0.368 0.376
Expression systems:
  • Saccharomyces cerevisiae
  • Escherichia coli