› 7cme

X-ray diffraction
2.45Å resolution

Crystal structure of human P-cadherin MEC12 (X dimer) in complex with 2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine (inhibitor)

Released:
DOI: 10.2210/pdb7cme/pdb
Model geometry
Fit model/data
PDB entry 7cme coloured by chain, front view.
PDB entry 7cme coloured by chain, side view.
PDB entry 7cme coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion
Senoo A, Ito S, Nagatoishi S, Saito Y, Ueno G, Kuroda D, Yoshida K, Tashima T, Kudo S, Sando S, Tsumoto K
Commun Biol 4 1041- (2021)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149555 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cadherin-3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 214 amino acids
Theoretical weight: 23.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P22223 (Residues: 108-320; Coverage: 27%)
Gene names: CDH3, CDHP
Sequence domains: Cadherin domain

Ligands and Environments

3 bound ligands:
Ligand DMS 2 x DMS
Ligand G60 3 x G60
Ligand CA 6 x CA
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: P212121
Unit cell:
a: 79.828Å b: 99.113Å c: 107.928Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.209 0.249
Expression system: Escherichia coli

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