SMTL ID : 5j5j.1

Crystal structure of a chimera of human Desmocollin-2 EC1 and human Desmoglein-2 EC2-EC5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.29 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- NAG: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]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-NAG-GAL-MAN-NAG.1: 3 residues within 4Å: Chain A: D.27, T.28, N.31 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.2: 7 residues within 4Å: Chain A: N.463, T.465, R.497, E.499, S.502, V.503, L.504 No protein-ligand interaction detected (PLIP)

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.3: 7 residues within 4Å: Chain A: N.258, F.259, T.260, N.305, K.306, A.307, A.308 No protein-ligand interaction detected (PLIP)

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

MAN.4: 4 residues within 4Å: Chain A: I.421, R.427, K.428, T.429 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.427 MAN.5: 7 residues within 4Å: Chain A: L.380, K.417, V.419, T.429, I.430, T.431 Ligands: MAN.6 No protein-ligand interaction detected (PLIP) MAN.6: 7 residues within 4Å: Chain A: S.340, V.341, K.417, T.431, G.432, T.433 Ligands: MAN.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.340, A:K.417, A:T.431

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

NAG.7: 1 residues within 4Å: Chain A: N.411 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.411 NAG.8: 4 residues within 4Å: Chain A: T.109, K.129, N.131, T.133 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.129 Hydrogen bonds: A:N.131

11 x CA: CALCIUM ION(Non-covalent)

CA.9: 5 residues within 4Å: Chain A: E.11, N.12, D.67, E.69, D.103 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.11, A:D.67, A:D.67, A:E.69, A:D.103 CA.10: 8 residues within 4Å: Chain A: E.11, R.68, E.69, D.100, I.101, D.103, N.104, D.136 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.69, A:D.100, A:I.101, A:D.103, A:D.136 CA.11: 8 residues within 4Å: Chain A: N.102, N.104, E.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.12: 5 residues within 4Å: Chain A: E.119, L.120, D.177, E.179, D.216 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.119, A:D.177, A:E.179, A:D.216 CA.13: 8 residues within 4Å: Chain A: E.119, R.178, E.179, D.213, V.214, D.216, N.217, D.248 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.119, A:E.179, A:E.179, A:D.213, A:D.248 CA.14: 8 residues within 4Å: Chain A: N.215, N.217, P.219, D.246, D.248, N.254, W.255, N.305 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.217, A:D.246, A:D.246, A:D.248, A:N.254 CA.15: 6 residues within 4Å: Chain A: E.232, E.292, N.330, V.331, E.333, D.368 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.232, A:E.292, A:V.331, A:E.333, A:D.368 CA.16: 6 residues within 4Å: Chain A: E.232, N.233, D.290, E.292, E.333, E.367 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.232, A:D.290, A:E.292, A:E.333, A:E.367 CA.17: 8 residues within 4Å: Chain A: E.348, F.404, E.405, D.440, I.441, D.443, N.444, D.470 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.348, A:E.405, A:E.405, A:I.441, A:D.470 CA.18: 5 residues within 4Å: Chain A: E.348, D.403, E.405, D.443, N.444 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.348, A:D.403, A:E.405, A:D.443 CA.19: 8 residues within 4Å: Chain A: N.442, N.444, C.445, D.468, D.470, N.474, S.475, D.523 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.444, A:D.468, A:D.470, A:N.474, A:D.523

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.20: 1 residues within 4Å: Chain A: K.318 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain A: S.479, F.480, Q.498 Ligand excluded by PLIP

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

2016-06-22

Peptides

Desmocollin-2,Desmoglein-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Desmocollin-2,Desmoglein-2