› 5ixc

X-ray diffraction
2.65Å resolution

Human GIVD cytosolic phospholipase A2 in complex with Methyl gamma-Linolenyl Fluorophosphonate

Released:
DOI: 10.2210/pdb5ixc/pdb
PDB entry 5ixc coloured by chain, front view.
PDB entry 5ixc coloured by chain, side view.
PDB entry 5ixc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of Human GIVD Cytosolic Phospholipase A2 Reveals Insights into Substrate Recognition.
Wang H, Klein MG, Snell G, Lane W, Zou H, Levin I, Li K, Sang BC
J Mol Biol 428 2769-79 (2016)
PMID: 27220631

Function and Biology Details

Reaction catalysed: 
Phosphatidylcholine + H(2)O = 1-acylglycerophosphocholine + a carboxylate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183254 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cytosolic phospholipase A2 delta Chains: A, B
Molecule details ›
Chains: A, B
Length: 814 amino acids
Theoretical weight: 91.44 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q86XP0 (Residues: 2-810; Coverage: 99%)
Gene name: PLA2G4D
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand 7FA 2 x 7FA
Ligand BA 6 x BA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P212121
Unit cell:
a: 100.567Å b: 111.379Å c: 157.645Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.237 0.251
Expression system: Spodoptera frugiperda

Quick links

Citations

1 citations in other articles

Structural basis of phosphatidylcholine recognition by the C2-domain of cytosolic phospholipase A2α.
Hirano et al. (2019)

1 mention without citation

Berberine Suppresses Colonic Inflammation in Dextran Sulfate Sodium-Induced Murine Colitis Through Inhibition of Cytosolic Phospholipase A2 Activity.
Zhai et al. (2020)