SMTL ID : 9jmj.1

Cryo-EM structure of the GD-BatCoV (BtCoV/Ii/GD/2014-422) RBD in complex with human DPP4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-mer

Ligands

7 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: I.305, N.307, Y.308, M.334 Chain C: N.159 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: N.205, T.207, Q.294, E.295, Y.316, E.318 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.316 Hydrogen bonds: A:E.318, A:E.318 NAG-NAG.4: 3 residues within 4Å: Chain A: W.173, V.265, N.267 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain B: N.205, T.207, Q.294, E.295, Y.316, E.318 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.316 Hydrogen bonds: B:E.318, B:E.318, B:E.318 NAG-NAG.6: 5 residues within 4Å: Chain B: I.180, Q.213, N.215, T.217, K.253 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: W.173, N.267 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 7 residues within 4Å: Chain B: I.305, N.307, M.334, S.335, T.336, R.582, D.664 No protein-ligand interaction detected (PLIP)

1 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: 7 residues within 4Å: Chain A: T.174, I.180, Q.213, N.215, T.217, E.218 Chain C: Q.186 No protein-ligand interaction detected (PLIP)

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

NAG.9: 3 residues within 4Å: Chain A: E.59, N.61, N.78 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain A: V.64, N.71, S.73 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.71, A:S.73 NAG.11: 2 residues within 4Å: Chain A: P.135, N.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.136 NAG.12: 2 residues within 4Å: Chain A: D.667, N.671 No protein-ligand interaction detected (PLIP) NAG.13: 4 residues within 4Å: Chain B: E.59, N.60, N.61, N.78 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.60, B:N.61, B:N.61, B:N.78 NAG.14: 2 residues within 4Å: Chain B: Y.69, N.71 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.69 NAG.15: 3 residues within 4Å: Chain B: R.583, D.667, N.671 No protein-ligand interaction detected (PLIP) NAG.16: 3 residues within 4Å: Chain B: R.133, P.135, N.136 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.133 Hydrogen bonds: B:N.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, H. et al., Structures and receptor binding activities of merbecovirus spike proteins reveal key signatures for human DPP4 adaptation. Sci Adv (2025)

Release Date

2025-06-18

Peptides

Dipeptidyl peptidase 4 soluble form,Isoform 1 of Immunoglobulin heavy constant gamma 1: AB
Spike glycoprotein,Isoform 1 of Immunoglobulin heavy constant gamma 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

Dipeptidyl peptidase 4 soluble form,Isoform 1 of Immunoglobulin heavy constant gamma 1

Spike glycoprotein,Isoform 1 of Immunoglobulin heavy constant gamma 1