SMTL ID : 8y8a.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

11 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 C: H.129, I.132, E.134, K.151, K.173, N.175 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:H.129 NAG-NAG.2: 4 residues within 4Å: Chain C: F.700, D.701, N.712, T.714 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain C: N.1198 Chain D: N.868 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.868 NAG-NAG.5: 2 residues within 4Å: Chain C: L.649, N.651 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain D: N.780 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain D: H.129, I.132, E.134, K.173, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain D: N.45 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain E: N.45 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain E: H.129, I.132, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain E: D.701, N.712, T.714, S.715 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain E: N.630, L.649, N.651 No protein-ligand interaction detected (PLIP)

2 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.4: 2 residues within 4Å: Chain C: D.4, N.119 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 1 residues within 4Å: Chain D: N.651 No protein-ligand interaction detected (PLIP)

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

NAG.14: 2 residues within 4Å: Chain C: N.6, N.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.6, C:N.9 NAG.15: 2 residues within 4Å: Chain C: N.179, S.181 No protein-ligand interaction detected (PLIP) NAG.16: 4 residues within 4Å: Chain C: G.604, Y.686, N.689, N.690 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.686 Hydrogen bonds: C:G.604, C:N.690 NAG.17: 1 residues within 4Å: Chain C: N.780 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.780 NAG.18: 4 residues within 4Å: Chain D: G.604, Y.686, N.689, N.690 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:N.689 Hydrogen bonds: D:N.690 NAG.19: 4 residues within 4Å: Chain D: S.719, P.756, F.757, N.758 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.757 Hydrogen bonds: D:S.719, D:P.756, D:N.758, D:N.758 NAG.20: 3 residues within 4Å: Chain D: N.179, S.181, A.182 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.179 NAG.21: 2 residues within 4Å: Chain E: N.179, S.181 No protein-ligand interaction detected (PLIP) NAG.22: 5 residues within 4Å: Chain C: D.867, N.868, Q.988 Chain E: V.1197, N.1198 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: E:V.1197 Hydrogen bonds: E:N.1198, C:D.867, C:N.868, C:Q.988 NAG.23: 7 residues within 4Å: Chain E: N.342, S.344, T.345, R.348, D.593, Y.596, S.597 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.342, E:S.344, E:T.345, E:R.348

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

Transmembrane protease serine 2: ABF
Spike glycoprotein: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
T

B
H

F
G

C
A

D
C

E
B

Transmembrane protease serine 2

Spike glycoprotein

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