SMTL ID : 1q5b.1

lambda-shaped TRANS and CIS interactions of cadherins model based on fitting C-cadherin (1L3W) to 3D map of desmosomes obtained by electron tomography

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: D.309, P.310, E.341, Y.342, T.343 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: D.377, T.400 Ligand excluded by PLIP NAG.3: 6 residues within 4Å: Chain A: Q.411, V.413, Y.414, I.426, T.427, T.428 Ligand excluded by PLIP NAG.5: 6 residues within 4Å: Chain A: R.417, T.456, T.469, T.471 Ligands: NDG.4, NAG.6 Ligand excluded by PLIP NAG.6: 7 residues within 4Å: Chain A: K.379, T.380, Q.454, S.470, T.471, T.473 Ligands: NAG.5 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: T.382, V.452, T.475 Ligands: NAG.12 Ligand excluded by PLIP NAG.8: 5 residues within 4Å: Chain A: Y.555, K.557, T.560, Y.561, T.562 Ligand excluded by PLIP NAG.9: 6 residues within 4Å: Chain A: L.566, T.568, V.574, G.575, T.576 Ligands: NAG.10 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: T.576, T.578 Ligands: NAG.9, NDG.11 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: Y.381, T.382, A.383, Q.395 Ligands: NAG.7 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.558 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.425 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: V.679, N.681 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain B: D.309, P.310, E.341, Y.342, T.343 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: D.377, T.400 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain B: Q.411, V.413, Y.414, I.426, T.427, T.428 Ligand excluded by PLIP NAG.32: 6 residues within 4Å: Chain B: R.417, T.456, T.469, T.471 Ligands: NDG.31, NAG.33 Ligand excluded by PLIP NAG.33: 7 residues within 4Å: Chain B: K.379, T.380, Q.454, S.470, T.471, T.473 Ligands: NAG.32 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: T.382, V.452, T.475 Ligands: NAG.39 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain B: Y.555, K.557, T.560, Y.561, T.562 Ligand excluded by PLIP NAG.36: 6 residues within 4Å: Chain B: L.566, T.568, V.574, G.575, T.576 Ligands: NAG.37 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: T.576, T.578 Ligands: NAG.36, NDG.38 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain B: Y.381, T.382, A.383, Q.395 Ligands: NAG.34 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.558 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.425 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: V.679, N.681 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain C: D.309, P.310, E.341, Y.342, T.343 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: D.377, T.400 Ligand excluded by PLIP NAG.57: 6 residues within 4Å: Chain C: Q.411, V.413, Y.414, I.426, T.427, T.428 Ligand excluded by PLIP NAG.59: 6 residues within 4Å: Chain C: R.417, T.456, T.469, T.471 Ligands: NDG.58, NAG.60 Ligand excluded by PLIP NAG.60: 7 residues within 4Å: Chain C: K.379, T.380, Q.454, S.470, T.471, T.473 Ligands: NAG.59 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain C: T.382, V.452, T.475 Ligands: NAG.66 Ligand excluded by PLIP NAG.62: 5 residues within 4Å: Chain C: Y.555, K.557, T.560, Y.561, T.562 Ligand excluded by PLIP NAG.63: 6 residues within 4Å: Chain C: L.566, T.568, V.574, G.575, T.576 Ligands: NAG.64 Ligand excluded by PLIP NAG.64: 4 residues within 4Å: Chain C: T.576, T.578 Ligands: NAG.63, NDG.65 Ligand excluded by PLIP NAG.66: 5 residues within 4Å: Chain C: Y.381, T.382, A.383, Q.395 Ligands: NAG.61 Ligand excluded by PLIP NAG.67: 1 residues within 4Å: Chain C: N.558 Ligand excluded by PLIP NAG.68: 1 residues within 4Å: Chain C: N.425 Ligand excluded by PLIP NAG.69: 2 residues within 4Å: Chain C: V.679, N.681 Ligand excluded by PLIP

6 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Post Translational Modification)

NDG.4: 4 residues within 4Å: Chain A: F.463, L.467, T.469 Ligands: NAG.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.458, A:L.467, A:L.467, A:T.469 NDG.11: 4 residues within 4Å: Chain A: A.490, I.564, T.580 Ligands: NAG.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.564 Hydrogen bonds: A:A.490, A:T.580 NDG.31: 4 residues within 4Å: Chain B: F.463, L.467, T.469 Ligands: NAG.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.458, B:L.467, B:L.467, B:T.469 NDG.38: 4 residues within 4Å: Chain B: A.490, I.564, T.580 Ligands: NAG.37 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.564 Hydrogen bonds: B:A.490, B:T.580 NDG.58: 4 residues within 4Å: Chain C: F.463, L.467, T.469 Ligands: NAG.59 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.458, C:L.467, C:L.467, C:T.469 NDG.65: 4 residues within 4Å: Chain C: A.490, I.564, T.580 Ligands: NAG.64 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.564 Hydrogen bonds: C:A.490, C:T.580

36 x CA: CALCIUM ION(Non-covalent)

CA.16: 6 residues within 4Å: Chain A: N.257, N.259, D.289, D.291, N.298, D.350 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.259, A:D.289, A:D.291, A:N.298, A:D.350 CA.17: 6 residues within 4Å: Chain A: E.166, E.224, D.255, Q.256, D.258, D.291 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.224, A:E.224, A:D.255, A:Q.256, A:D.291 CA.18: 5 residues within 4Å: Chain A: E.166, N.167, D.222, E.224, D.258 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.166, A:D.222, A:E.224, A:D.258 CA.19: 7 residues within 4Å: Chain A: E.274, R.336, E.337, D.368, A.369, D.371, D.403 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.274, A:D.368, A:D.368, A:D.371, A:D.403 CA.20: 4 residues within 4Å: Chain A: E.274, D.335, E.337, D.371 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.274, A:D.335, A:E.337, A:D.371 CA.21: 6 residues within 4Å: Chain A: N.370, N.372, D.401, D.403, A.409, N.459 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.372, A:D.401, A:D.401, A:D.403, A:A.409 CA.22: 6 residues within 4Å: Chain A: E.387, D.444, F.445, E.446, E.483 Ligands: CA.26 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.387, A:D.444, A:D.444, A:E.446, A:E.483 CA.23: 6 residues within 4Å: Chain A: N.482, E.483, D.513, D.515, Q.520, D.569 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.483, A:D.513, A:D.515, A:D.569, A:D.569 CA.24: 5 residues within 4Å: Chain A: E.498, D.550, E.552, D.590 Ligands: CA.27 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.498, A:E.498, A:D.550, A:D.590, A:D.590 CA.25: 6 residues within 4Å: Chain A: N.589, N.591, D.616, D.618, N.622, D.670 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:N.591, A:D.616, A:D.618, A:D.670 CA.26: 7 residues within 4Å: Chain A: E.387, E.446, D.480, V.481, E.483, D.515 Ligands: CA.22 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.446, A:D.480, A:V.481, A:E.483, A:D.515 CA.27: 7 residues within 4Å: Chain A: E.498, E.552, D.587, V.588, D.590, D.618 Ligands: CA.24 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.498, A:E.552, A:E.552, A:V.588, A:D.590 CA.43: 6 residues within 4Å: Chain B: N.257, N.259, D.289, D.291, N.298, D.350 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.259, B:D.289, B:D.291, B:N.298, B:D.350 CA.44: 6 residues within 4Å: Chain B: E.166, E.224, D.255, Q.256, D.258, D.291 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.224, B:E.224, B:D.255, B:Q.256, B:D.291 CA.45: 5 residues within 4Å: Chain B: E.166, N.167, D.222, E.224, D.258 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.166, B:D.222, B:E.224, B:D.258 CA.46: 7 residues within 4Å: Chain B: E.274, R.336, E.337, D.368, A.369, D.371, D.403 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.274, B:D.368, B:D.368, B:D.371, B:D.403 CA.47: 4 residues within 4Å: Chain B: E.274, D.335, E.337, D.371 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.274, B:D.335, B:E.337, B:D.371 CA.48: 6 residues within 4Å: Chain B: N.370, N.372, D.401, D.403, A.409, N.459 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.372, B:D.401, B:D.401, B:D.403, B:A.409 CA.49: 6 residues within 4Å: Chain B: E.387, D.444, F.445, E.446, E.483 Ligands: CA.53 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.387, B:D.444, B:D.444, B:E.446, B:E.483 CA.50: 6 residues within 4Å: Chain B: N.482, E.483, D.513, D.515, Q.520, D.569 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.483, B:D.513, B:D.515, B:D.569, B:D.569 CA.51: 5 residues within 4Å: Chain B: E.498, D.550, E.552, D.590 Ligands: CA.54 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.498, B:E.498, B:D.550, B:D.590, B:D.590 CA.52: 6 residues within 4Å: Chain B: N.589, N.591, D.616, D.618, N.622, D.670 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:N.591, B:D.616, B:D.618, B:D.670 CA.53: 7 residues within 4Å: Chain B: E.387, E.446, D.480, V.481, E.483, D.515 Ligands: CA.49 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.446, B:D.480, B:V.481, B:E.483, B:D.515 CA.54: 7 residues within 4Å: Chain B: E.498, E.552, D.587, V.588, D.590, D.618 Ligands: CA.51 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.498, B:E.552, B:E.552, B:V.588, B:D.590 CA.70: 6 residues within 4Å: Chain C: N.257, N.259, D.289, D.291, N.298, D.350 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:N.259, C:D.289, C:D.291, C:N.298, C:D.350 CA.71: 6 residues within 4Å: Chain C: E.166, E.224, D.255, Q.256, D.258, D.291 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.224, C:E.224, C:D.255, C:Q.256, C:D.291 CA.72: 5 residues within 4Å: Chain C: E.166, N.167, D.222, E.224, D.258 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.166, C:D.222, C:E.224, C:D.258 CA.73: 7 residues within 4Å: Chain C: E.274, R.336, E.337, D.368, A.369, D.371, D.403 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.274, C:D.368, C:D.368, C:D.371, C:D.403 CA.74: 4 residues within 4Å: Chain C: E.274, D.335, E.337, D.371 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.274, C:D.335, C:E.337, C:D.371 CA.75: 6 residues within 4Å: Chain C: N.370, N.372, D.401, D.403, A.409, N.459 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:N.372, C:D.401, C:D.401, C:D.403, C:A.409 CA.76: 6 residues within 4Å: Chain C: E.387, D.444, F.445, E.446, E.483 Ligands: CA.80 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.387, C:D.444, C:D.444, C:E.446, C:E.483 CA.77: 6 residues within 4Å: Chain C: N.482, E.483, D.513, D.515, Q.520, D.569 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.483, C:D.513, C:D.515, C:D.569, C:D.569 CA.78: 5 residues within 4Å: Chain C: E.498, D.550, E.552, D.590 Ligands: CA.81 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.498, C:E.498, C:D.550, C:D.590, C:D.590 CA.79: 6 residues within 4Å: Chain C: N.589, N.591, D.616, D.618, N.622, D.670 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:N.591, C:D.616, C:D.618, C:D.670 CA.80: 7 residues within 4Å: Chain C: E.387, E.446, D.480, V.481, E.483, D.515 Ligands: CA.76 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.446, C:D.480, C:V.481, C:E.483, C:D.515 CA.81: 7 residues within 4Å: Chain C: E.498, E.552, D.587, V.588, D.590, D.618 Ligands: CA.78 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.498, C:E.552, C:E.552, C:V.588, C:D.590

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, W. et al., Untangling Desmosomal Knots with Electron Tomography. Science (2003)

Release Date

2003-10-07

Peptides

EP-cadherin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

EP-cadherin

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