› 6m5m

X-ray diffraction
1.7Å resolution

SPL-1 - GlcNAc complex

Released:
DOI: 10.2210/pdb6m5m/pdb
PDB entry 6m5m coloured by chain, front view.
PDB entry 6m5m coloured by chain, side view.
PDB entry 6m5m coloured by chain, top view.
Source organism: Saxidomus purpurata
Primary publication:
Novel carbohydrate-recognition mode of the invertebrate C-type lectin SPL-1 from Saxidomus purpuratus revealed by the GlcNAc-complex crystal in the presence of Ca2.
Unno H, Higuchi S, Goda S, Hatakeyama T
Acta Crystallogr F Struct Biol Commun 76 271-277 (2020)
PMID: 32510468

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-104604 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
C-type lectin domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 158 amino acids
Theoretical weight: 17.98 KDa
Source organism: Saxidomus purpurata
UniProt:
  • Canonical: A0A2Z6G7U6 (Residues: 1-158; Coverage: 100%)
Gene name: SPL-A
Sequence domains: Lectin C-type domain
C-type lectin domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 159 amino acids
Theoretical weight: 17.9 KDa
Source organism: Saxidomus purpurata
UniProt:
  • Canonical: A0A2Z6G7U3 (Residues: 1-159; Coverage: 100%)
Gene name: SPL-B
Sequence domains: Lectin C-type domain

Ligands and Environments

2 bound ligands:
Ligand CA 4 x CA
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P65
Unit cell:
a: 44.46Å b: 44.46Å c: 303.613Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.204 0.203 0.216

Quick links

Citations

1 review citation

Functional Diversity of Novel Lectins with Unique Structural Features in Marine Animals.
Hatakeyama et al. (2023)

1 mention without citation

Novel carbohydrate-recognition mode of the invertebrate C-type lectin SPL-1 from Saxidomus purpuratus revealed by the GlcNAc-complex crystal in the presence of Ca2.
Unno et al. (2020)