4kyi

X-ray diffraction
3.08Å resolution

Crystal structure of the phospholipase VipD from Legionella pneumophila in complex with the human GTPase Rab5

Released:

Function and Biology Details

Reaction catalysed:
GTP + H(2)O = GDP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-156303 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
PNPLA domain-containing protein Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 551 amino acids
Theoretical weight: 61.23 KDa
Source organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5ZRP9 (Residues: 19-564; Coverage: 88%)
Gene names: lpg2831, vipD
Sequence domains: Patatin-like phospholipase
Structure domains: Cytosolic phospholipase A2 catalytic domain
Ras-related protein Rab-5C Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 170 amino acids
Theoretical weight: 18.79 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P51148 (Residues: 18-182; Coverage: 76%)
Gene names: RAB5C, RABL
Sequence domains: Ras family
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P1
Unit cell:
a: 94.275Å b: 97.976Å c: 109.849Å
α: 76.57° β: 80.71° γ: 78.91°
R-values:
R R work R free
0.235 0.233 0.28
Expression system: Escherichia coli