SMTL ID : 5jym.1

Human P-cadherin EC12 with scFv TSP11 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-2-2-mer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.11, D.67, E.69, D.103 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.11, A:D.67, A:E.69, A:D.103, H2O.1 CA.2: 6 residues within 4Å: Chain A: E.11, E.69, D.100, Q.101, D.103, D.136 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.11, A:D.100, A:Q.101, A:D.103, A:D.136 CA.3: 6 residues within 4Å: Chain A: N.102, H.104, D.134, D.136, N.143, D.195 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.104, A:D.134, A:D.136, A:N.143, A:D.195 CA.4: 1 residues within 4Å: Chain A: D.44 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.44, H2O.2 CA.5: 6 residues within 4Å: Chain C: E.11, E.69, D.100, Q.101, D.103, D.136 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.11, C:D.100, C:Q.101, C:D.103, C:D.136 CA.6: 6 residues within 4Å: Chain C: N.102, H.104, D.134, D.136, N.143, D.195 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.104, C:D.134, C:D.136, C:N.143, C:D.195 CA.7: 4 residues within 4Å: Chain C: E.11, D.67, E.69, D.103 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.11, C:D.67, C:E.69, C:D.103, H2O.3, H2O.4 CA.8: 1 residues within 4Å: Chain C: T.109 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2016-12-28

Peptides

Cadherin-3: AC
Antibody scFv TSP11: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Cadherin-3

Antibody scFv TSP11

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