SMTL ID : 6l8q.1

Complex structure of bat CD26 and MERS-RBD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-4-4-mer

Ligands

13 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: N.181, T.183, K.267, E.268, Y.289 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.289 NAG-NAG.3: 4 residues within 4Å: Chain A: I.278, N.280, S.308, R.555 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: R.412, N.455, T.457, Y.460 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain C: N.181, T.183, N.234, K.267, E.268, Y.289 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.289 NAG-NAG.7: 3 residues within 4Å: Chain C: I.278, N.280, S.308 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: R.412, N.455, T.457, Y.460 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain E: N.47 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain E: N.181, T.183, K.267, E.268, Y.289, E.291 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.289 NAG-NAG.18: 3 residues within 4Å: Chain E: I.278, N.280, D.637 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain E: R.412, N.455, T.457, Y.460 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.460 NAG-NAG.22: 6 residues within 4Å: Chain G: N.181, T.183, F.184, K.267, E.268, Y.289 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:F.184, G:Y.289 NAG-NAG.24: 4 residues within 4Å: Chain G: I.278, N.280, S.308, A.309 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain G: R.412, I.436, N.455, T.457, Y.460 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Y.460

4 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.2: 8 residues within 4Å: Chain A: I.156, N.191, T.193, D.194, K.229 Chain B: W.169, E.170, D.173 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.173 NAG-NAG-BMA.6: 8 residues within 4Å: Chain C: I.156, N.191, T.193, D.194, K.229 Chain D: W.169, E.170, D.173 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.173 NAG-NAG-BMA.17: 7 residues within 4Å: Chain E: I.156, N.191, T.193, D.194, K.229 Chain F: W.169, E.170 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 7 residues within 4Å: Chain G: I.156, N.191, T.193, D.194, K.229 Chain H: W.169, E.170 No protein-ligand interaction detected (PLIP)

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

NAG.9: 3 residues within 4Å: Chain A: L.40, N.47, S.49 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.40 Hydrogen bonds: A:N.47, A:S.49 NAG.10: 4 residues within 4Å: Chain A: E.35, N.36, N.37, N.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.36, A:N.37, A:N.54 NAG.11: 5 residues within 4Å: Chain B: N.44, T.46, K.47, K.221, L.222 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.221 Hydrogen bonds: B:N.44, B:K.221 NAG.12: 1 residues within 4Å: Chain C: N.47 No protein-ligand interaction detected (PLIP) NAG.13: 4 residues within 4Å: Chain C: E.35, N.36, N.37, N.54 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.36, C:N.37, C:N.54 NAG.14: 5 residues within 4Å: Chain D: N.44, T.46, K.47, K.221, L.222 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.221 Hydrogen bonds: D:N.44 NAG.20: 4 residues within 4Å: Chain E: E.35, N.36, N.37, N.54 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.37, E:N.54 NAG.21: 5 residues within 4Å: Chain F: N.44, T.46, K.47, K.221, L.222 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:K.221 Hydrogen bonds: F:N.44 NAG.26: 2 residues within 4Å: Chain G: N.47, S.49 No protein-ligand interaction detected (PLIP) NAG.27: 4 residues within 4Å: Chain G: E.35, N.36, N.37, N.54 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.37, G:N.54 NAG.28: 5 residues within 4Å: Chain H: N.44, T.46, K.47, K.221, L.222 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:K.221 Hydrogen bonds: H:N.44, H:K.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, Y. et al., Molecular Basis of Binding between Middle East Respiratory Syndrome Coronavirus and CD26 from Seven Bat Species. J.Virol. (2020)

Release Date

2019-12-04

Peptides

Dipeptidyl peptidase 4: ACEG
Spike glycoprotein: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

Dipeptidyl peptidase 4

Spike glycoprotein

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