SMTL ID : 3q2v.1

Crystal structure of mouse E-cadherin ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-dimer

Ligands

24 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.11, N.12, D.67, E.69, D.103 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.11, A:D.67, A:E.69, A:D.103 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:E.69, A:E.69, A:D.100, A:D.103 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.4: 4 residues within 4Å: Chain A: E.119, D.180, E.182, D.216 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.119, A:D.180, A:D.216 CA.5: 6 residues within 4Å: Chain A: E.119, E.182, D.213, I.214, D.216, D.248 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.119, A:E.182, A:D.213, A:I.214, A:D.248 CA.6: 6 residues within 4Å: Chain A: N.215, N.217, D.246, D.248, A.254, N.304 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.217, A:D.246, A:D.246, A:D.248, A:A.254 CA.7: 6 residues within 4Å: Chain A: E.232, E.291, D.325, V.326, E.328, D.360 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.291, A:D.325, A:V.326, A:E.328, A:D.360 CA.8: 4 residues within 4Å: Chain A: E.232, D.289, E.291, E.328 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.232, A:D.289, A:E.291, A:E.328, A:E.328 CA.9: 8 residues within 4Å: Chain A: N.327, E.328, P.330, E.358, D.360, Q.365, D.415, A.421 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.328, A:E.358, A:D.360, A:D.415 CA.10: 6 residues within 4Å: Chain A: E.343, D.395, E.397, D.436, N.437 Ligands: CA.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.343, A:D.395, A:E.397, A:D.436 CA.11: 8 residues within 4Å: Chain A: E.343, E.397, D.433, V.434, D.436, N.437, D.464 Ligands: CA.10 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.343, A:E.397, A:D.433, A:D.436, A:D.464 CA.12: 6 residues within 4Å: Chain A: N.435, N.437, D.462, D.464, N.468, D.517 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.437, A:D.462, A:D.462, A:D.464, A:N.468 CA.23: 6 residues within 4Å: Chain B: E.11, N.12, D.67, E.69, D.103, N.104 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.11, B:D.67, B:D.67, B:E.69, B:D.103 CA.24: 7 residues within 4Å: Chain B: E.11, R.68, E.69, D.100, Q.101, D.103, D.136 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.11, B:E.69, B:D.100, B:D.103, B:D.136 CA.25: 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.134, B:D.136, B:N.143 CA.26: 4 residues within 4Å: Chain B: E.119, D.180, E.182, D.216 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.119, B:D.180, B:E.182, B:D.216 CA.27: 6 residues within 4Å: Chain B: E.119, E.182, D.213, I.214, D.216, D.248 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.182, B:D.213, B:I.214, B:D.216, B:D.248 CA.28: 6 residues within 4Å: Chain B: N.215, N.217, D.246, D.248, A.254, N.304 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:N.217, B:D.246, B:D.248, B:A.254 CA.29: 7 residues within 4Å: Chain B: E.232, E.291, D.325, V.326, E.328, D.360 Ligands: CA.30 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.232, B:E.291, B:E.291, B:D.360 CA.30: 6 residues within 4Å: Chain B: E.232, D.289, F.290, E.291, E.328 Ligands: CA.29 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.291, B:E.328 CA.31: 8 residues within 4Å: Chain B: N.327, E.328, P.330, E.358, P.359, D.360, Q.365, D.415 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.328, B:E.358, B:D.360, B:D.415 CA.32: 6 residues within 4Å: Chain B: E.343, E.397, D.433, V.434, D.464 Ligands: CA.34 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.343, B:E.397, B:D.464 CA.33: 2 residues within 4Å: Chain B: D.462, D.464 No protein-ligand interaction detected (PLIP) CA.34: 4 residues within 4Å: Chain B: E.343, D.395, E.397 Ligands: CA.32 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.343, B:D.395, B:E.397

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.13: 2 residues within 4Å: Chain A: C.9, E.13 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.13, A:E.13 MN.35: 2 residues within 4Å: Chain B: C.9, E.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.13, B:E.13

18 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.14: 2 residues within 4Å: Chain A: S.126, M.128 No protein-ligand interaction detected (PLIP) MAN.15: 5 residues within 4Å: Chain A: K.129, S.131, A.132, T.133, Y.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.129, A:Y.148, A:Y.148 MAN.16: 2 residues within 4Å: Chain A: T.204, K.206 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.204, A:K.206 MAN.17: 5 residues within 4Å: Chain A: V.262, H.299, R.301, P.314, T.316 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.301, A:P.314 MAN.18: 3 residues within 4Å: Chain A: S.224, T.316, T.318 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.224 MAN.19: 1 residues within 4Å: Chain A: T.355 No protein-ligand interaction detected (PLIP) MAN.20: 4 residues within 4Å: Chain A: W.372, I.412, T.422 Ligands: MAN.21 No protein-ligand interaction detected (PLIP) MAN.21: 6 residues within 4Å: Chain A: W.372, T.422, G.423, T.424 Ligands: MAN.20, MAN.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.422 MAN.22: 4 residues within 4Å: Chain A: E.336, T.424, T.426 Ligands: MAN.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.336, A:T.424 MAN.36: 4 residues within 4Å: Chain B: S.126, V.127, M.128, V.171 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.128 Water bridges: B:S.126 MAN.37: 3 residues within 4Å: Chain B: K.129, S.131, A.132 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.129 MAN.38: 3 residues within 4Å: Chain B: V.190, T.204, K.206 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.205, B:K.206 MAN.39: 3 residues within 4Å: Chain B: R.301, P.314, T.316 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.316 MAN.40: 6 residues within 4Å: Chain B: S.224, T.225, H.299, T.316, A.317, T.318 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.317 MAN.41: 2 residues within 4Å: Chain B: T.355, A.356 No protein-ligand interaction detected (PLIP) MAN.42: 2 residues within 4Å: Chain B: I.420, T.422 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.414, B:I.420 MAN.43: 3 residues within 4Å: Chain B: T.422, T.424 Ligands: MAN.44 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.422 MAN.44: 4 residues within 4Å: Chain B: A.335, E.336, T.426 Ligands: MAN.43 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harrison, O.J. et al., The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins. Structure (2011)

Release Date

2011-04-06

Peptides

Cadherin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cadherin-1