SMTL ID : 4zmy.1

Crystal structure of human P-cadherin (monomer 1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

14 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 6 residues within 4Å: Chain A: E.12, E.70, D.101, Q.102, D.104, D.137 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:E.12, A:E.70, A:D.101, A:Q.102, A:D.104, A:D.137 CA.2: 6 residues within 4Å: Chain A: N.103, H.105, D.135, D.137, N.144, D.196 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.105, A:D.135, A:D.137, A:N.144, A:D.196 CA.3: 4 residues within 4Å: Chain A: E.12, D.68, E.70, D.104 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.12, A:D.68, A:E.70, A:D.104, H2O.2, H2O.8 CA.4: 2 residues within 4Å: Chain A: E.120 Ligands: CA.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.120, H2O.1, H2O.9, H2O.11 CA.5: 1 residues within 4Å: Chain A: E.70 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.70, H2O.4, H2O.6, H2O.9, H2O.9 CA.6: 1 residues within 4Å: Chain A: D.214 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.214, H2O.3, H2O.8, H2O.10, H2O.11 CA.7: 1 residues within 4Å: Ligands: CA.4 No protein-ligand interaction detected (PLIP) CA.8: 6 residues within 4Å: Chain B: E.12, E.70, D.101, Q.102, D.104, D.137 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:E.12, B:E.70, B:D.101, B:Q.102, B:D.104, B:D.137 CA.9: 6 residues within 4Å: Chain B: N.103, H.105, D.135, D.137, N.144, D.196 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.105, B:D.135, B:D.137, B:N.144, B:D.196 CA.10: 4 residues within 4Å: Chain B: E.12, D.68, E.70, D.104 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.12, B:D.68, B:E.70, B:D.104, H2O.13, H2O.19 CA.11: 2 residues within 4Å: Chain B: E.120 Ligands: CA.14 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.120, H2O.12, H2O.20, H2O.22 CA.12: 1 residues within 4Å: Chain B: E.70 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.70, H2O.15, H2O.17, H2O.20, H2O.20 CA.13: 1 residues within 4Å: Chain B: D.214 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.214, H2O.14, H2O.19, H2O.20, H2O.22 CA.14: 1 residues within 4Å: Ligands: CA.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kudo, S. et al., Adhesive Dimerization of Human P-Cadherin Catalyzed by a Chaperone-like Mechanism. Structure (2016)

Release Date

2016-09-07

Peptides

Cadherin-3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cadherin-3