› 5xsz

X-ray diffraction
3.2Å resolution

Crystal structure of zebrafish lysophosphatidic acid receptor LPA6

Released:
DOI: 10.2210/pdb5xsz/pdb
PDB entry 5xsz coloured by chain, front view.
PDB entry 5xsz coloured by chain, side view.
PDB entry 5xsz coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into ligand recognition by the lysophosphatidic acid receptor LPA6.
Taniguchi R, Inoue A, Sayama M, Uwamizu A, Yamashita K, Hirata K, Yoshida M, Tanaka Y, Kato HE, Nakada-Nakura Y, Otani Y, Nishizawa T, Doi T, Ohwada T, Ishitani R, Aoki J, Nureki O
Nature 548 356-360 (2017)
PMID: 28792932

Function and Biology Details

Reaction catalysed: 
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133004 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endolysin; G-protein coupled receptors family 1 profile domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 477 amino acids
Theoretical weight: 54.39 KDa
Source organisms: Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q08BG4 (Residues: 1-227, 233-312; Coverage: 86%)
  • Canonical: P00720 (Residues: 2-161; Coverage: 98%)
Gene names: E, lpar6, lpar6a, zgc:153784
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand OLC 3 x OLC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: P212121
Unit cell:
a: 55.88Å b: 65.02Å c: 160.65Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.236 0.263
Expression system: Spodoptera frugiperda

Quick links

Citations

16 review citations

Role of lysophosphatidic acid and its receptors in health and disease: novel therapeutic strategies.
Geraldo et al. (2021)
15 more

19 mentions without citation

Exploring G Protein-Coupled Receptors (GPCRs) Ligand Space via Cheminformatics Approaches: Impact on Rational Drug Design.
Basith et al. (2018)
18 more