SMTL ID : 8y8b.1

Local structure of HCoV-HKU1C spike in complex with TMPRSS2 and glycan

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 3 residues within 4Å: Chain A: D.4, N.119, T.141 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.2: 2 residues within 4Å: Chain A: N.6, N.9 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: I.132, K.173, N.175 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 2 residues within 4Å: Chain A: N.179, S.181 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: T.236, D.237, N.238 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: N.318, W.319, N.322, S.324, R.334 Ligands: NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: L.649, N.651 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 8 residues within 4Å: Chain B: N.342, S.344, T.345, R.348, N.592, D.593, Y.596, S.597 No protein-ligand interaction detected (PLIP)

1 x MJJ: methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid(Non-covalent)

MJJ.9: 10 residues within 4Å: Chain A: N.13, Y.15, T.18, L.66, K.67, S.69, Y.71, W.76, I.232, S.233 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.66, A:Y.71, A:W.76, A:W.76 Hydrogen bonds: A:N.13, A:K.67, A:S.69, A:I.232, A:S.233 Salt bridges: A:K.67

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

NAG.10: 1 residues within 4Å: Chain A: N.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.16 NAG.11: 3 residues within 4Å: Chain A: I.156, R.157, N.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.158 NAG.12: 2 residues within 4Å: Chain A: V.100, N.101 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.100 NAG.13: 1 residues within 4Å: Chain B: N.441 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.441 NAG.14: 2 residues within 4Å: Chain B: V.419, N.420 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.420

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: AB
Transmembrane protease serine 2: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
T

Spike glycoprotein

Transmembrane protease serine 2

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