SMTL ID : 5erd.1

Crystal structure of human Desmoglein-2 ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: S.16, N.19, P.20, V.54, E.61, N.63 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: T.111, K.131, N.133, T.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 7 residues within 4Å: Chain B: T.111, Q.112, F.115, M.130, K.131, I.132, N.133 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- FUC: 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-FUC.3: 7 residues within 4Å: Chain A: I.451, N.465, T.467, R.499, E.501, S.504, L.506 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 4 residues within 4Å: Chain B: N.19, P.20, V.54, N.63 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: N.260, F.261, T.262, I.274, E.275, T.276 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 7 residues within 4Å: Chain B: N.465, T.467, R.499, E.501, S.504, V.505, L.506 No protein-ligand interaction detected (PLIP)

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

NAG.8: 1 residues within 4Å: Chain A: N.413 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.413 NAG.9: 4 residues within 4Å: Chain A: N.260, F.261, T.262, K.308 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.260 NAG.28: 2 residues within 4Å: Chain B: Q.412, N.413 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.413

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

MAN.10: 4 residues within 4Å: Chain A: I.423, R.429, K.430, T.431 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.429 MAN.11: 7 residues within 4Å: Chain A: L.382, K.419, V.421, T.431, I.432, T.433 Ligands: MAN.12 No protein-ligand interaction detected (PLIP) MAN.12: 7 residues within 4Å: Chain A: S.342, V.343, K.419, T.433, G.434, T.435 Ligands: MAN.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.342, A:K.419 MAN.25: 4 residues within 4Å: Chain B: I.423, R.429, K.430, T.431 No protein-ligand interaction detected (PLIP) MAN.26: 7 residues within 4Å: Chain B: L.382, E.383, K.419, V.421, T.431, I.432, T.433 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.431, B:T.431, B:T.433 MAN.27: 6 residues within 4Å: Chain B: S.342, V.343, K.419, T.433, G.434, T.435 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.419, B:T.433

22 x CA: CALCIUM ION(Non-covalent)

CA.13: 8 residues within 4Å: Chain A: E.11, R.70, E.71, D.102, I.103, D.105, D.138 Ligands: CA.14 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.11, A:E.71, A:D.102, A:I.103, A:D.138 CA.14: 5 residues within 4Å: Chain A: E.11, D.69, E.71, D.105 Ligands: CA.13 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.69, A:D.69, A:E.71, A:D.105, H2O.3 CA.15: 8 residues within 4Å: Chain A: N.104, N.106, E.107, P.108, D.136, D.138, N.144, D.194 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.106, A:D.136, A:D.138, A:N.144, A:D.194 CA.16: 9 residues within 4Å: Chain A: E.121, R.180, E.181, D.215, V.216, D.218, N.219, D.250 Ligands: CA.17 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.121, A:E.181, A:E.181, A:D.215, A:D.250 CA.17: 6 residues within 4Å: Chain A: E.121, D.179, E.181, D.218, N.219 Ligands: CA.16 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.121, A:D.179, A:E.181, A:D.218, H2O.1 CA.18: 8 residues within 4Å: Chain A: N.217, N.219, P.221, D.248, D.250, N.256, W.257, N.307 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.219, A:D.248, A:D.248, A:D.250, A:N.256 CA.19: 8 residues within 4Å: Chain A: E.350, F.406, E.407, D.442, I.443, D.445, D.472 Ligands: CA.23 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.350, A:E.407, A:D.442, A:D.445, A:D.472 CA.20: 7 residues within 4Å: Chain A: N.444, N.446, C.447, D.470, D.472, N.476, D.525 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.446, A:D.470, A:D.470, A:D.472, A:D.525 CA.21: 7 residues within 4Å: Chain A: E.234, E.294, N.332, V.333, E.335, D.370 Ligands: CA.22 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.234, A:E.294, A:V.333, A:E.335, A:D.370 CA.22: 7 residues within 4Å: Chain A: E.234, D.292, Y.293, E.294, E.335, E.369 Ligands: CA.21 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.234, A:D.292, A:E.294, A:E.335, A:E.369 CA.23: 6 residues within 4Å: Chain A: E.350, D.405, E.407, D.445, N.446 Ligands: CA.19 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.405, A:E.407, A:D.445, A:D.445, H2O.1 CA.29: 8 residues within 4Å: Chain B: E.11, R.70, E.71, D.102, I.103, D.105, D.138 Ligands: CA.37 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.11, B:E.71, B:D.102, B:I.103, B:D.138 CA.30: 7 residues within 4Å: Chain B: N.104, N.106, D.136, D.138, N.144, S.145, D.194 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.106, B:D.136, B:D.138, B:N.144, B:D.194 CA.31: 8 residues within 4Å: Chain B: E.121, R.180, E.181, D.215, V.216, D.218, N.219, D.250 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.121, B:E.181, B:E.181, B:D.215, B:D.250 CA.32: 8 residues within 4Å: Chain B: N.217, N.219, P.221, D.248, D.250, N.256, W.257, N.307 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.219, B:D.248, B:D.248, B:D.250, B:N.256 CA.33: 6 residues within 4Å: Chain B: E.350, D.405, E.407, D.445, N.446 Ligands: CA.39 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.405, B:E.407, B:D.445, B:D.445, H2O.5 CA.34: 8 residues within 4Å: Chain B: N.444, N.446, C.447, D.470, D.472, N.476, S.477, D.525 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.446, B:D.470, B:D.472, B:N.476, B:D.525 CA.35: 5 residues within 4Å: Chain B: E.121, D.179, E.181, D.218, N.219 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.121, B:D.179, B:E.181, B:D.218, H2O.5 CA.36: 8 residues within 4Å: Chain B: E.234, Y.293, E.294, N.332, V.333, E.335, D.370 Ligands: CA.38 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.234, B:E.294, B:V.333, B:E.335, B:D.370 CA.37: 6 residues within 4Å: Chain B: E.11, D.69, R.70, E.71, D.105 Ligands: CA.29 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.11, B:D.69, B:E.71, B:D.105, H2O.6 CA.38: 7 residues within 4Å: Chain B: E.234, D.292, Y.293, E.294, E.335, E.369 Ligands: CA.36 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.292, B:E.294, B:E.335, B:E.369, H2O.4 CA.39: 8 residues within 4Å: Chain B: E.350, F.406, E.407, D.442, I.443, D.445, D.472 Ligands: CA.33 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.350, B:E.407, B:I.443, B:D.445, B:D.472

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

EDO.24: 2 residues within 4Å: Chain A: R.86, G.87 No protein-ligand interaction detected (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

Desmoglein-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Desmoglein-2