› 5jym

X-ray diffraction
2.45Å resolution

Human P-cadherin EC12 with scFv TSP11 bound

Released:
DOI: 10.2210/pdb5jym/pdb
PDB entry 5jym coloured by chain, front view.
PDB entry 5jym coloured by chain, side view.
PDB entry 5jym coloured by chain, top view.
Source organisms:
Primary publication:
Disruption of cell adhesion by an antibody targeting the cell-adhesive intermediate (X-dimer) of human P-cadherin.
Kudo S, Caaveiro JM, Nagatoishi S, Miyafusa T, Matsuura T, Sudou Y, Tsumoto K
Sci Rep 7 39518 (2017)
PMID: 28045038

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-235078 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cadherin-3 Chains: A, C
Molecule details ›
Chains: A, C
Length: 213 amino acids
Theoretical weight: 23.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P22223 (Residues: 108-320; Coverage: 27%)
Gene names: CDH3, CDHP
Sequence domains: Cadherin domain
Structure domains: Cadherins
Antibody scFv TSP11 Chains: B, D
Molecule details ›
Chains: B, D
Length: 257 amino acids
Theoretical weight: 27.51 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)

Ligands and Environments

1 bound ligand:
Ligand CA 8 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Unit cell:
a: 58.7Å b: 83.43Å c: 199.82Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.223 0.27
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Engineering the Interactions of Classical Cadherin Cell-Cell Adhesion Proteins.
Sivasankar et al. (2023)
9 other articles

2 mentions without citation

Disruption of cell adhesion by an antibody targeting the cell-adhesive intermediate (X-dimer) of human P-cadherin.
Kudo et al. (2017)
1 more