› 5izr

X-ray diffraction
3.25Å resolution

Human GIVD cytosolic phospholipase A2 in complex with Methyl gamma-Linolenyl Fluorophosphonate inhibitor and Terbium Chloride

Released:
DOI: 10.2210/pdb5izr/pdb
PDB entry 5izr coloured by chain, front view.
PDB entry 5izr coloured by chain, side view.
PDB entry 5izr 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, C, D
Molecule details ›
Chains: A, B, C, D
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 4 x 7FA
Ligand TB 15 x TB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P21
Unit cell:
a: 100.824Å b: 112.667Å c: 159.2Å
α: 90° β: 90.03° γ: 90°
R-values:
R R work R free
0.232 0.23 0.267
Expression system: Spodoptera frugiperda

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Citations

2 citation in other articles

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