SMTL ID : 5eqx.1

Crystal structure of human Desmoglein-3 ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

monomer

Ligands

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.1: 6 residues within 4Å: Chain A: S.16, N.19, P.20, V.52, D.54, N.61 No protein-ligand interaction detected (PLIP)

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

NAG.2: 5 residues within 4Å: Chain A: S.109, Q.110, F.113, N.131, T.133 No protein-ligand interaction detected (PLIP)

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 7 residues within 4Å: Chain A: E.11, R.68, E.69, D.100, I.101, D.103, D.136 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.11, A:E.69, A:D.100, A:I.101, A:D.136 CA.4: 8 residues within 4Å: Chain A: N.212, N.214, P.216, D.243, D.245, N.251, W.252, N.302 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.214, A:D.243, A:D.243, A:D.245, A:N.251 CA.5: 5 residues within 4Å: Chain A: E.11, D.67, E.69, D.103, N.104 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.11, A:D.67, A:E.69, A:D.103, H2O.2 CA.6: 8 residues within 4Å: Chain A: N.102, N.104, P.105, P.106, D.134, D.136, N.142, D.192 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.104, A:D.134, A:D.136, A:N.142, A:D.192 CA.7: 5 residues within 4Å: Chain A: E.119, N.120, D.177, E.179, D.213 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.119, A:D.177, A:E.179, A:D.213 CA.8: 7 residues within 4Å: Chain A: E.119, R.178, E.179, D.210, V.211, D.213, D.245 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.119, A:E.179, A:D.210, A:V.211, A:D.245 CA.9: 6 residues within 4Å: Chain A: E.229, E.289, N.327, V.328, E.330, D.366 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.229, A:E.289, A:V.328, A:E.330 CA.10: 7 residues within 4Å: Chain A: E.229, N.230, D.287, Y.288, E.289, E.330, E.365 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.229, A:D.287, A:E.289, A:E.330, A:E.330

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

MAN.11: 7 residues within 4Å: Chain A: E.416, L.418, T.427, S.428, T.429 Ligands: MAN.12, MAN.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.427 MAN.12: 8 residues within 4Å: Chain A: A.337, S.338, E.416, T.429, G.430, T.431, Y.433 Ligands: MAN.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.433, A:Y.433 MAN.13: 5 residues within 4Å: Chain A: L.418, I.420, G.425, T.427 Ligands: MAN.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.425

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harrison, O.J. et al., Structural basis of adhesive binding by desmocollins and desmogleins. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-06-15

Peptides

Desmoglein-3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Desmoglein-3