SMTL ID : 8y89.1

Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 2TMPRSS2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-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: 3 residues within 4Å: Chain A: D.4, V.118, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: I.132, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.651 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: D.701, N.712, T.714, S.715 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.45, E.259 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.45, E.259 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.630, L.649, N.651 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain B: F.700, D.701, N.712, T.714, S.715 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: N.179, S.181 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: N.630, N.651 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.11: 1 residues within 4Å: Chain C: N.780 No protein-ligand interaction detected (PLIP)

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

NAG.12: 2 residues within 4Å: Chain A: N.179, S.181 No protein-ligand interaction detected (PLIP) NAG.13: 6 residues within 4Å: Chain A: G.604, V.605, S.685, Y.686, N.689, N.690 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.604, A:N.689 NAG.14: 1 residues within 4Å: Chain A: N.780 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain A: N.1198 Chain B: D.867, P.967 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.867, B:P.967 Hydrogen bonds: B:D.867, A:N.1198 NAG.16: 3 residues within 4Å: Chain B: S.719, P.756, N.758 No protein-ligand interaction detected (PLIP) NAG.17: 1 residues within 4Å: Chain B: N.780 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.780 NAG.18: 2 residues within 4Å: Chain B: E.907, N.911 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.911 NAG.19: 5 residues within 4Å: Chain B: S.1196, N.1198 Chain C: D.867, N.868, Q.988 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:S.1196, B:N.1198, C:N.868, C:N.868 Hydrophobic interactions: C:D.867 NAG.20: 6 residues within 4Å: Chain C: N.342, S.344, T.345, N.592, D.593, Y.596 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.342, C:S.344, C:T.345 NAG.21: 3 residues within 4Å: Chain C: E.907, A.908, N.911 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.908 Hydrogen bonds: C:E.907 NAG.22: 4 residues within 4Å: Chain C: D.701, N.712, T.714, S.715 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.712 NAG.23: 3 residues within 4Å: Chain A: D.867 Chain C: V.1197, N.1198 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.1197 Hydrogen bonds: C:N.1198, A:D.867 NAG.24: 1 residues within 4Å: Chain C: N.45 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., TMPRSS2 and glycan receptors synergistically facilitate coronavirus entry. Cell (2024)

Release Date

2024-07-17

Peptides

Spike glycoprotein: ABC
Transmembrane protease serine 2: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
T

E
G

Spike glycoprotein

Transmembrane protease serine 2

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