SMTL ID : 7ev1.1

Crystal structure of LI-Cadherin EC1-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: N.92, N.94, D.124, D.126, N.132, D.187 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.94, A:D.124, A:D.126, A:N.132, A:D.187 CA.2: 8 residues within 4Å: Chain A: E.12, E.59, D.90, I.91, D.93, N.94, D.126 Ligands: CA.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.12, A:D.90, A:I.91, A:D.93, A:D.126 CA.3: 5 residues within 4Å: Chain A: E.12, D.57, E.59, D.93 Ligands: CA.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.12, A:D.57, A:E.59, A:D.93, H2O.9, H2O.9 CA.5: 6 residues within 4Å: Chain B: N.92, N.94, D.124, D.126, N.132, D.187 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.94, B:D.124, B:D.126, B:N.132, B:D.187 CA.6: 8 residues within 4Å: Chain B: E.12, E.59, D.90, I.91, D.93, N.94, D.126 Ligands: CA.7 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.12, B:D.90, B:I.91, B:D.93, B:D.126 CA.7: 5 residues within 4Å: Chain B: E.12, D.57, E.59, D.93 Ligands: CA.6 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.12, B:D.57, B:E.59, B:D.93, H2O.20, H2O.21

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 2 residues within 4Å: Chain A: E.45, E.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.47 Water bridges: A:E.47

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.148, B:N.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yui, A. et al., Mechanism of dimerization and structural features of human LI-cadherin. J.Biol.Chem. (2021)

Release Date

2021-06-16

Peptides

Cadherin-17: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cadherin-17