SMTL ID : 7cym.1

Crystal structure of LI-Cadherin EC1-4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 8 residues within 4Å: Chain A: N.228, D.277, D.313, N.314, P.315, T.317, F.407 Ligands: CA.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.314 NAG-NAG-BMA-MAN.3: 9 residues within 4Å: Chain B: E.227, N.228, L.276, D.277, D.313, P.315, T.317, F.407 Ligands: CA.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.317

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain A: T.363, P.364, Q.395, N.397, Q.414 No protein-ligand interaction detected (PLIP)

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 3 residues within 4Å: Chain A: L.105, N.127, T.164 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.127, A:N.127 NAG.5: 2 residues within 4Å: Chain A: Y.142, N.162 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.142 Hydrogen bonds: A:N.162 NAG.12: 2 residues within 4Å: Chain B: Y.142, N.162 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.142 Hydrogen bonds: B:N.162

12 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: N.98, N.100, D.130, D.132, N.138, D.193 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.100, A:D.130, A:D.132, A:N.138, A:D.193 CA.7: 7 residues within 4Å: Chain A: E.18, E.65, D.96, I.97, D.99, N.100, D.132 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.65, A:D.96, A:I.97, A:D.99, A:D.132 CA.8: 4 residues within 4Å: Chain A: E.18, D.63, E.65, D.99 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.18, A:D.63, A:E.65, A:D.99 CA.9: 5 residues within 4Å: Chain A: E.227, D.277, E.279, D.313 Ligands: NAG-NAG-BMA-MAN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.227, A:D.277, A:E.279, A:D.313 CA.10: 6 residues within 4Å: Chain A: E.227, E.279, D.310, I.311, D.313, D.346 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.227, A:E.279, A:D.310, A:I.311, A:D.346 CA.11: 6 residues within 4Å: Chain A: N.312, N.314, D.344, D.346, N.352, D.404 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.314, A:D.344, A:D.346, A:N.352, A:D.404 CA.13: 7 residues within 4Å: Chain B: E.18, E.65, D.96, I.97, D.99, N.100, D.132 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.18, B:E.65, B:D.96, B:I.97, B:D.99 CA.14: 4 residues within 4Å: Chain B: E.18, D.63, E.65, D.99 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.18, B:D.63, B:E.65, B:D.99, H2O.2 CA.15: 6 residues within 4Å: Chain B: N.98, N.100, D.130, D.132, N.138, D.193 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.100, B:D.130, B:D.132, B:N.138, B:D.193 CA.16: 7 residues within 4Å: Chain B: E.227, E.279, D.310, I.311, D.313, D.346 Ligands: CA.17 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.227, B:E.279, B:D.310, B:I.311, B:D.313 CA.17: 6 residues within 4Å: Chain B: E.227, D.277, E.279, D.313 Ligands: NAG-NAG-BMA-MAN.3, CA.16 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.227, B:D.277, B:E.279, B:D.313, H2O.1 CA.18: 6 residues within 4Å: Chain B: N.312, N.314, D.344, D.346, N.352, D.404 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.314, B:D.344, B:D.346, B:N.352, B:D.404

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

2021-08-18

Peptides

Cadherin-17: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cadherin-17