SMTL ID : 8wde.1

CryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN (composite map)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

3 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.1: 6 residues within 4Å: Chain A: N.48, F.60, H.186, Y.188, R.193, Y.223 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.60, A:Y.223 NAG-NAG-BMA.3: 5 residues within 4Å: Chain B: N.48, F.60, H.186, R.193, Y.223 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.60, B:Y.223 NAG-NAG-BMA.5: 7 residues within 4Å: Chain C: L.46, T.47, N.48, H.186, Y.188, R.193, Y.223 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.186

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

NAG-NAG.2: 5 residues within 4Å: Chain A: N.229, S.231, A.236, N.237, F.255 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.229, S.231, A.236, F.255 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.229, S.231, A.236 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain D: R.575, N.616, W.896 No protein-ligand interaction detected (PLIP)

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

NAG.8: 2 residues within 4Å: Chain A: N.84, T.86 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: V.274, N.426, T.428 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.504, E.515 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: G.509, S.511, N.524 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.657, T.789 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain B: Y.82, F.83, N.84, T.86 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: Y.130, N.157, S.166 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: N.504, E.515 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: V.496, G.509, N.524 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.657, S.659 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain C: N.84, T.86 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain C: Y.130, N.157, T.164, S.166 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain C: N.504, V.513 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: G.509, F.510, N.524 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: N.657, S.659 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: D.697, N.700, K.703 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain D: K.176, S.190, N.200 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: S.393 Chain D: N.254 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain D: D.368, Q.531, L.559, N.560 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain E: D.368, N.560 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsai, Y.X. et al., Molecular basis of host recognition of human coronavirus 229E. Nat Commun (2025)

Release Date

2025-03-05

Peptides

Spike glycoprotein: ABC
Aminopeptidase N: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Spike glycoprotein

Aminopeptidase N