SMTL ID : 3qrb.2 (1 other biounit)

crystal structure of E-cadherin EC1-2 P5A P6A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.10, H2O.10 CA.2: 8 residues within 4Å: Chain A: E.11, E.69, D.100, Q.101, D.103, N.104, D.136 Ligands: CA.1 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, 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.7: 5 residues within 4Å: Chain B: E.11, D.67, E.69, D.103 Ligands: CA.8 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.11, B:D.67, B:E.69, B:D.103, H2O.26, H2O.27 CA.8: 8 residues within 4Å: Chain B: E.11, E.69, D.100, Q.101, D.103, N.104, D.136 Ligands: CA.7 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.11, B:D.100, B:Q.101, B:D.103, B:D.136 CA.9: 6 residues within 4Å: Chain B: N.102, N.104, D.134, D.136, N.143, D.195 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.104, B:D.134, B:D.136, B:N.143, B:D.195

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

EDO.4: 3 residues within 4Å: Chain A: Y.77, H.79, P.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.79 EDO.5: 4 residues within 4Å: Chain A: W.2, M.92 Chain B: W.2 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.2 Water bridges: A:I.4 EDO.10: 3 residues within 4Å: Chain B: Y.77, H.79, P.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.79 EDO.11: 4 residues within 4Å: Chain A: W.2 Chain B: W.2, M.92 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.2 Water bridges: B:I.4

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 5 residues within 4Å: Chain A: D.138, V.139, N.140, T.141, Y.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.138 PGE.12: 5 residues within 4Å: Chain B: D.138, V.139, N.140, T.141, Y.142 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vendome, J. et al., Molecular design principles underlying beta-strand swapping in the adhesive dimerization of cadherins. Nat.Struct.Mol.Biol. (2011)

Release Date

2011-05-18

Peptides

Cadherin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Cadherin-1

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