SMTL ID : 9k9n.1

Cryo-EM structure of MjHKU4r-CoV-1 receptor-binding domain complexed with human CD26

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.61 Å

Oligo State

hetero-2-1-mer

Ligands

4 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: 4 residues within 4Å: Chain A: Y.77, N.79, S.80, S.81 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.77 NAG-NAG.2: 3 residues within 4Å: Chain A: W.181, V.273, N.275 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: Y.77, N.79, S.81 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: I.313, N.315, M.342, S.343, T.344 Chain C: H.147 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(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-MAN.4: 11 residues within 4Å: Chain B: I.188, Q.221, N.223, T.225 Chain C: S.168, Y.170, G.171, F.172, S.173, E.174, E.177 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.177

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

NAG-NAG-FUC.5: 3 residues within 4Å: Chain B: W.181, V.273, N.275 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain A: E.67, N.69, N.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.69, A:N.86 NAG.8: 3 residues within 4Å: Chain A: I.142, P.143, N.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.144 NAG.9: 4 residues within 4Å: Chain A: N.213, T.215, Q.302, E.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.213, A:T.215, A:E.303 NAG.10: 5 residues within 4Å: Chain A: I.188, Q.221, N.223, T.225, E.226 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.188 Hydrogen bonds: A:E.226 NAG.11: 1 residues within 4Å: Chain A: N.315 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.311 NAG.12: 5 residues within 4Å: Chain A: L.513, N.514, F.518, R.575, D.599 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.513, A:F.518 Hydrogen bonds: A:N.514, A:R.575 NAG.13: 4 residues within 4Å: Chain B: E.67, N.68, N.69, N.86 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.69, B:N.86 NAG.14: 3 residues within 4Å: Chain B: I.142, P.143, N.144 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.144 NAG.15: 3 residues within 4Å: Chain B: N.213, T.215, E.303 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.303 NAG.16: 3 residues within 4Å: Chain B: L.513, N.514, R.575 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.513 Hydrogen bonds: B:N.514, B:R.575

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Rational design of human CD26 receptor for a strong neutralizing ability against MjHKU4r-CoV-1 and MERS-CoV. Hlife (2025)

Release Date

2025-09-03

Peptides

Dipeptidyl peptidase 4 soluble form: AB
Spike protein S1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Dipeptidyl peptidase 4 soluble form

Spike protein S1