SMTL ID : 9jmm.1

Cryo-EM structure of the SE-PangolinCoV (MjHKU4r-CoV-1) RBD in complex with human DPP4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-mer

Ligands

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.1: 11 residues within 4Å: Chain A: I.180, Q.213, N.215, T.217, E.218 Chain C: S.183, Y.185, G.186, S.188, E.189, E.192 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.188

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.2: 7 residues within 4Å: Chain A: I.305, N.307, M.334, S.335, T.336, D.664 Chain C: H.162 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain A: N.205, T.207, F.208, Q.294, E.295, Y.316, E.318 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.208, A:Y.316 Hydrogen bonds: A:E.295, 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: 7 residues within 4Å: Chain B: N.205, T.207, F.208, Q.294, E.295, Y.316, E.318 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.208, B:Y.316 Hydrogen bonds: B:E.318, B:E.318 NAG-NAG.6: 5 residues within 4Å: Chain B: I.180, Q.213, N.215, T.217, E.218 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: W.173, V.265, N.267 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain B: I.305, N.307, M.334, S.335, T.336, D.664 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:D.664

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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.61 NAG.10: 3 residues within 4Å: Chain A: N.66, N.71, S.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.66 NAG.11: 4 residues within 4Å: Chain A: R.133, I.134, P.135, N.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.133, A:N.136 NAG.12: 1 residues within 4Å: Chain A: N.671 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.671 NAG.13: 4 residues within 4Å: Chain B: E.59, N.60, N.61, N.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.60, B:N.61 NAG.14: 2 residues within 4Å: Chain B: Y.69, N.71 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.69 Hydrogen bonds: B:N.71 NAG.15: 4 residues within 4Å: Chain B: R.583, D.667, H.668, N.671 No protein-ligand interaction detected (PLIP) NAG.16: 4 residues within 4Å: Chain B: R.133, I.134, P.135, N.136 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.133, B:N.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, H. et al., The complex of SE-PangolinCoV-RBD and human DPP4. To Be Published

Release Date

2025-06-18

Peptides

Dipeptidyl peptidase 4 soluble form: 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

Spike glycoprotein,Isoform 1 of Immunoglobulin heavy constant gamma 1