› 5yrk

X-ray diffraction
1.35Å resolution

Crystal structure of PPL3C

Released:
DOI: 10.2210/pdb5yrk/pdb
PDB entry 5yrk coloured by chain, front view.
PDB entry 5yrk coloured by chain, side view.
PDB entry 5yrk coloured by chain, top view.
Source organism: Pteria penguin
Primary publication:
Structures of jacalin-related lectin PPL3 regulating pearl shell biomineralization.
Nakae S, Shionyu M, Ogawa T, Shirai T
Proteins 86 644-653 (2018)
PMID: 29524263

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-104594 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Jacalin-type lectin domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 142 amino acids
Theoretical weight: 15.72 KDa
Source organism: Pteria penguin
UniProt:
  • Canonical: A0A2Z5V8U8 (Residues: 20-161; Coverage: 100%)
Gene name: PPL3-b
Sequence domains: Jacalin-like lectin domain

Ligands and Environments

1 bound ligand:
Ligand SO4 8 x SO4
1 modified residue:
Ligand PCA 2 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P212121
Unit cell:
a: 40.25Å b: 73.79Å c: 90.5Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.179 0.206

Quick links

Citations

4 citation in other articles

Biochemical and Initial Structural Characterization of the Monocot Chimeric Jacalin OsJAC1.
Huwa et al. (2021)
3 more

1 mention without citation

Glycan Binding Profiling of Jacalin-Related Lectins from the Pteria Penguin Pearl Shell.
Ogawa et al. (2019)