› 4fom

X-ray diffraction
3.93Å resolution

Crystal structure of human nectin-3 full ectodomain (D1-D3)

Released:
DOI: 10.2210/pdb4fom/pdb
PDB entry 4fom coloured by chain, front view.
PDB entry 4fom coloured by chain, side view.
PDB entry 4fom coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Nectin ectodomain structures reveal a canonical adhesive interface.
Harrison OJ, Vendome J, Brasch J, Jin X, Hong S, Katsamba PS, Ahlsen G, Troyanovsky RB, Troyanovsky SM, Honig B, Shapiro L
Nat Struct Mol Biol 19 906-15 (2012)
PMID: 22902367

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192511 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Nectin-3 Chain: A
Molecule details ›
Chain: A
Length: 308 amino acids
Theoretical weight: 34.04 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9NQS3 (Residues: 58-359; Coverage: 61%)
Gene names: NECTIN3, PRR3, PVRL3
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN, FUC
Carbohydrate polymer
1 bound ligand:
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4C
Spacegroup: P6522
Unit cell:
a: 131.867Å b: 131.867Å c: 247.543Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.248 0.247 0.279
Expression system: Homo sapiens

Quick links

Citations

17 review citations

Mechanobiology of collective cell behaviours.
Ladoux et al. (2017)
16 more

3 mentions without citation

Nectin ectodomain structures reveal a canonical adhesive interface.
Harrison et al. (2012)
2 more