SMTL ID : 8yzi.1

The structure of PDCoV RBD and dog APN complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

9 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 C: N.57, N.205, R.223, E.239 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.223 NAG-NAG.2: 7 residues within 4Å: Chain C: S.55, N.57, R.81, N.205, R.223, T.242 Ligands: NAG-NAG.1 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.81 NAG-NAG.4: 3 residues within 4Å: Chain C: Q.609, T.650, N.654 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: W.494, N.498 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain D: N.57, R.223, E.239 Ligands: NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain D: S.55, N.57, R.81, N.205, T.242 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain D: D.404, N.598, I.629 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain D: Q.609, P.648, T.650, L.651, N.654 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain D: S.473, W.494, N.498 No protein-ligand interaction detected (PLIP)

1 x NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-BMA.3: 2 residues within 4Å: Chain C: D.404, N.598 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.404

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

NAG.11: 2 residues within 4Å: Chain A: N.15, N.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.15, A:N.50 NAG.12: 3 residues within 4Å: Chain B: Q.13, N.15, N.50 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.13, B:Q.13 NAG.13: 3 residues within 4Å: Chain C: N.99, G.155, E.156 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.156 NAG.14: 6 residues within 4Å: Chain C: H.210, S.212, L.214, S.226, P.228, N.236 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.212, C:L.214 NAG.15: 2 residues within 4Å: Chain C: N.791, T.792 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.793 NAG.17: 3 residues within 4Å: Chain D: N.99, G.155, E.156 No protein-ligand interaction detected (PLIP) NAG.18: 5 residues within 4Å: Chain D: S.212, L.214, S.226, P.228, N.236 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.212

2 x ZN: ZINC ION(Non-covalent)

ZN.16: 3 residues within 4Å: Chain C: H.359, H.363, E.382 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.359, C:H.363, C:E.382 ZN.19: 4 residues within 4Å: Chain D: E.326, H.359, H.363, E.382 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.359, D:H.363, D:E.382, D:E.382

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tian, Y. et al., Cross-species recognition of two porcine coronaviruses to their cellular receptor aminopeptidase N of dogs and seven other species. Plos Pathog. (2025)

Release Date

2024-12-11

Peptides

Spike protein: AB
Aminopeptidase N: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
D

Spike protein

Aminopeptidase N