SMTL ID : 6cxy.1

Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody Fab mAb-1_19A11

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: N.102, N.104, D.134, D.136, N.143, D.195 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.104, A:D.134, A:D.136, A:N.143, A:D.195 CA.2: 8 residues within 4Å: Chain A: E.11, E.69, D.100, Q.101, D.103, N.104, D.136 Ligands: CA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.11, A:E.69, A:E.69, A:D.100, A:D.136 CA.3: 5 residues within 4Å: Chain A: E.11, D.67, E.69, D.103 Ligands: CA.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.11, A:D.67, A:E.69, A:D.103, H2O.4, H2O.8

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: W.2, V.3, I.4, M.92 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: E.13, G.15, P.16, F.17, K.19 Chain C: R.99 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain B: P.41, T.90, A.91, M.92, S.114, V.115, T.116 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain B: R.66, S.84, Q.86, D.88, D.89 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain B: Y.59, K.64, L.67 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: V.48, G.49, T.63, E.64 Chain B: R.31, Y.100, Y.104 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: N.161, S.162, T.200, N.202 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain B: Q.111, G.112 Chain C: G.47 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Chain B: L.11 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: S.28, L.29, S.30, N.73 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: E.46, W.47, N.60 Chain C: T.103, F.104 Ligands: EDO.20 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain C: S.71, G.72 Ligands: EDO.17 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain C: S.58, I.69, G.70, S.71 Ligands: EDO.16 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain C: L.30, S.32, Q.35 Ligand excluded by PLIP EDO.19: 1 residues within 4Å: Chain C: L.30 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain C: F.104 Ligands: EDO.15 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain C: Q.44, K.45, P.46, G.47, Q.48 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain C: I.150, N.151, V.152, N.167, W.169 Ligand excluded by PLIP

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 4 residues within 4Å: Chain A: D.138, N.140, T.141, Y.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.138 Water bridges: A:Y.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dranow, D.M. et al., Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody Fab mAb-1_19A11. to be published

Release Date

2019-04-10

Peptides

Cadherin-1: A
Heavy chain: B
Light Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
H

C
L

Cadherin-1

Heavy chain

Light Chain