› 5jyl

X-ray diffraction
2.55Å resolution

Human P-cadherin MEC1 with scFv TSP7 bound

Released:
DOI: 10.2210/pdb5jyl/pdb
PDB entry 5jyl coloured by chain, front view.
PDB entry 5jyl coloured by chain, side view.
PDB entry 5jyl 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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-235077 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cadherin-3 Chains: A, C
Molecule details ›
Chains: A, C
Length: 101 amino acids
Theoretical weight: 11.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P22223 (Residues: 108-207; Coverage: 12%)
Gene names: CDH3, CDHP
Sequence domains: Cadherin domain
Structure domains: Cadherins
scFv TSP7 Chains: B, D
Molecule details ›
Chains: B, D
Length: 253 amino acids
Theoretical weight: 27.35 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)

Ligands and Environments

3 bound ligands:
Ligand GOL 1 x GOL
Ligand PO4 1 x PO4
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P21
Unit cell:
a: 66.57Å b: 49.41Å c: 111.66Å
α: 90° β: 101.89° γ: 90°
R-values:
R R work R free
0.217 0.214 0.271
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)
7 other articles

4 mentions without citation

Chemical Diversification of Simple Synthetic Antibodies.
Islam et al. (2021)
3 more