SMTL ID : 6vel.1

Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody 66E8Fab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-1-1-1-mer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: Y.51, G.118, N.119, Y.120, Y.121, D.123 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.119, A:Y.120, A:Y.121 SO4.2: 7 residues within 4Å: Chain A: Y.120, Y.121 Chain B: Y.51, H.110 Chain C: K.219, S.316, T.317 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.69 Salt bridges: B:H.110, C:K.219 SO4.3: 5 residues within 4Å: Chain B: E.112, Y.113 Chain C: G.314, L.315, S.316 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.316, B:Y.113 Water bridges: C:S.316, C:S.316 SO4.4: 4 residues within 4Å: Chain B: Q.56, K.64, F.81, D.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.56, B:D.101 Salt bridges: B:K.64 SO4.7: 4 residues within 4Å: Chain C: W.116, V.117, I.118, M.206 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.117 Water bridges: C:V.117 SO4.8: 5 residues within 4Å: Chain A: G.50, Y.51 Chain C: V.304, T.318 Ligands: SO4.1 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.318, A:N.119

3 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain C: E.125, D.181, E.183, D.217 Ligands: CA.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.125, C:D.181, C:E.183, C:D.217, H2O.4 CA.6: 6 residues within 4Å: Chain C: N.216, N.218, D.248, D.250, N.257, D.309 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:N.218, C:D.248, C:D.250, C:N.257, C:D.309 CA.9: 7 residues within 4Å: Chain C: E.125, E.183, D.214, Q.215, D.217, D.250 Ligands: CA.5 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.125, C:D.214, C:Q.215, C:D.217, C:D.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maker, A. et al., Regulation of multiple dimeric states of E-cadherin by adhesion activating antibodies revealed through Cryo-EM and X-ray crystallography. Pnas Nexus (2022)

Release Date

2020-01-29

Peptides

66E8 Fab Heavy Chain: A
66E8 Fab Light Chain: B
Ubiquitin-like protein SMT3,Cadherin-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
C

66E8 Fab Heavy Chain

66E8 Fab Light Chain

Ubiquitin-like protein SMT3,Cadherin-1