› 3u83

X-ray diffraction
2.5Å resolution

Crystal structure of nectin-1

Released:
DOI: 10.2210/pdb3u83/pdb
PDB entry 3u83 coloured by chain, front view.
PDB entry 3u83 coloured by chain, side view.
PDB entry 3u83 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Binding of herpes simplex virus glycoprotein D to nectin-1 exploits host cell adhesion.
Zhang N, Yan J, Lu G, Guo Z, Fan Z, Wang J, Shi Y, Qi J, Gao GF
Nat Commun 2 577 (2011)
PMID: 22146396

Function and Biology Details

Biochemical function:
  • not assigned
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-172234 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nectin-1 Chain: A
Molecule details ›
Chain: A
Length: 331 amino acids
Theoretical weight: 36.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15223 (Residues: 30-335; Coverage: 63%)
Gene names: HVEC, NECTIN1, PRR1, PVRL1
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand PG6 1 x PG6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: R32
Unit cell:
a: 127.52Å b: 127.52Å c: 190.555Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.187 0.185 0.23
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Herpes virus fusion and entry: a story with many characters.
Eisenberg et al. (2012)
13 more

7 mentions without citation

Binding mode of the side-by-side two-IgV molecule CD226/DNAM-1 to its ligand CD155/Necl-5.
Wang et al. (2019)
6 more