SMTL ID : 4kr0.1

Complex structure of MERS-CoV spike RBD bound to CD26

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-mer

Ligands

8 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: 5 residues within 4Å: Chain A: V.45, Y.50, N.52, S.53, S.54 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.50 NAG-NAG.2: 8 residues within 4Å: Chain A: N.186, T.188, F.189, N.239, Q.275, E.276, Y.297, E.299 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.189, A:Y.297 Hydrogen bonds: A:E.276, A:E.299, A:E.299 NAG-NAG.4: 3 residues within 4Å: Chain A: W.154, V.246, N.248 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.154 NAG-NAG.5: 7 residues within 4Å: Chain A: I.286, N.288, M.315, S.316, T.317, R.563, D.645 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain C: V.45, Y.50, N.52, S.53, S.54 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.50 NAG-NAG.9: 8 residues within 4Å: Chain C: N.186, T.188, F.189, N.239, Q.275, E.276, Y.297, E.299 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.189, C:Y.297 Hydrogen bonds: C:E.276, C:E.276, C:E.299 NAG-NAG.11: 3 residues within 4Å: Chain C: W.154, V.246, N.248 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.154 NAG-NAG.12: 7 residues within 4Å: Chain C: I.286, N.288, M.315, S.316, T.317, R.563, D.645 No protein-ligand interaction detected (PLIP)

2 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.3: 8 residues within 4Å: Chain A: I.161, Q.194, N.196, T.198, E.199, K.234 Chain B: W.174, E.175 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.178 Water bridges: B:E.175 NAG-NAG-BMA.10: 8 residues within 4Å: Chain C: I.161, Q.194, N.196, T.198, E.199, K.234 Chain D: W.174, E.175 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.178 Water bridges: D:E.175

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

NAG.6: 3 residues within 4Å: Chain A: R.114, I.115, N.117 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.114 Hydrogen bonds: A:N.117 NAG.7: 4 residues within 4Å: Chain A: E.40, N.41, N.42, N.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.41, A:N.42 NAG.13: 3 residues within 4Å: Chain C: R.114, I.115, N.117 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:R.114 Hydrogen bonds: C:N.117 NAG.14: 4 residues within 4Å: Chain C: E.40, N.41, N.42, N.59 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.41, C:N.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, G. et al., Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26. Nature (2013)

Release Date

2013-07-10

Peptides

Dipeptidyl peptidase 4: AC
S protein: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Dipeptidyl peptidase 4

S protein

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