SMTL ID : 9daz.1

Molecular basis of pathogenicity of the recently emerged FCoV-23 coronavirus. Complex of fAPN with FCoV-23 RBD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

10 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: 6 residues within 4Å: Chain A: N.606, K.610, P.645, T.647, L.648, N.651 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.53, I.75, N.202, R.220 Ligands: NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain A: S.51, N.53, R.77, N.202, R.220, T.239 Ligands: NAG-NAG.2, NAG-NAG.2 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: D.401, N.595 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: D.45, L.61, N.63, F.100 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain C: N.606, K.610, P.645, T.647, L.648, N.651 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain C: N.53, I.75, N.202, R.220 Ligands: NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 8 residues within 4Å: Chain C: S.51, N.53, R.77, N.202, R.220, T.239 Ligands: NAG-NAG.8, NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: D.401, N.595 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain D: D.45, L.61, N.63, F.100 No protein-ligand interaction detected (PLIP)

2 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: 5 residues within 4Å: Chain A: N.709, E.737 Chain B: Y.53, Q.55, I.57 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.53, A:E.737 Hydrogen bonds: B:Q.55 NAG-NAG-FUC.11: 5 residues within 4Å: Chain C: N.709, E.737 Chain D: Y.53, Q.55, I.57 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:E.737, D:Y.53 Hydrogen bonds: D:Q.55

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

NAG.13: 3 residues within 4Å: Chain A: N.95, Q.151, G.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.151 NAG.15: 3 residues within 4Å: Chain C: N.95, Q.151, G.152 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.151

2 x ZN: ZINC ION(Non-covalent)

ZN.14: 3 residues within 4Å: Chain A: H.356, H.360, E.379 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.356, A:H.360, A:E.379 ZN.16: 3 residues within 4Å: Chain C: H.356, H.360, E.379 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.356, C:H.360, C:E.379

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tortorici, M.A. et al., Loss of FCoV-23 spike domain 0 enhances fusogenicity and entry kinetics. Nature (2025)

Release Date

2025-07-09

Peptides

Aminopeptidase N,Immunoglobulin gamma-1 heavy chain: AC
Spike glycoprotein: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Aminopeptidase N,Immunoglobulin gamma-1 heavy chain

Spike glycoprotein