› 1dji

X-ray diffraction
2.5Å resolution

PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH CALCIUM

Released:
DOI: 10.2210/pdb1dji/pdb
PDB entry 1dji coloured by chain, front view.
PDB entry 1dji coloured by chain, side view.
PDB entry 1dji coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
A ternary metal binding site in the C2 domain of phosphoinositide-specific phospholipase C-delta1.
Essen LO, Perisic O, Lynch DE, Katan M, Williams RL
Biochemistry 36 2753-62 (1997)
PMID: 9062102

Function and Biology Details

Reaction catalysed: 
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1D-myo-inositol 1,4,5-trisphosphate + diacylglycerol
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145423 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 624 amino acids
Theoretical weight: 70.57 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P10688 (Residues: 133-756; Coverage: 83%)
Gene name: Plcd1
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand CA 6 x CA
Ligand ACT 2 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX9.6
Spacegroup: F4132
Unit cell:
a: 398.03Å b: 398.03Å c: 398.03Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.22 0.28
Expression system: Escherichia coli

Quick links

Citations

26 review citations

Synthesis and function of 3-phosphorylated inositol lipids.
Vanhaesebroeck et al. (2001)
25 more

5 mentions without citation

Structural bioinformatics prediction of membrane-binding proteins.
Bhardwaj et al. (2006)
4 more