› 4jjh

X-ray diffraction
2.25Å resolution

Crystal structure of the D1 domain from human Nectin-4 extracellular fragment [PSI-NYSGRC-005624]

Released:
DOI: 10.2210/pdb4jjh/pdb
PDB entry 4jjh coloured by chain, front view.
PDB entry 4jjh coloured by chain, side view.
PDB entry 4jjh coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Kumar PR, Bonanno J, Ahmed M, Banu R, Bhosle R, Calarese D, Celikigil A, Chamala S, Chan MK, Chowdhury S, Fiser A, Garforth S, Glenn AS, Hillerich B, Khafizov K, Love J, Patel H, Seidel R, Stead M, Toro R, Nathenson SG, Almo SC, New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-188651 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Processed poliovirus receptor-related protein 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 133 amino acids
Theoretical weight: 14.44 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q96NY8 (Residues: 32-153; Coverage: 26%)
Gene names: LNIR, NECTIN4, PRR4, PVRL4
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P41
Unit cell:
a: 35.193Å b: 35.193Å c: 205.331Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.222 0.292
Expression system: Trichoplusia ni

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