SMTL ID : 8y8j.1

Local structure of HCoV-HKU1C spike in complex with glycan

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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.1: 5 residues within 4Å: Chain A: D.4, F.5, N.119, T.141, D.164 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.2: 3 residues within 4Å: Chain A: H.129, I.132, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.179, S.181 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: S.234, N.235, T.236, D.237, N.238 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: L.649, N.651 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain B: N.342, S.344, T.345, R.348, D.593, Y.596, S.597 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.344

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

MJJ.7: 10 residues within 4Å: Chain A: N.13, Y.15, L.66, K.67, S.69, Y.71, L.72, S.73, W.76, S.233 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.15, A:L.66, A:W.76 Hydrogen bonds: A:N.13, A:Y.15, A:K.67, A:S.69 Salt bridges: A:K.67

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

NAG.8: 2 residues within 4Å: Chain A: N.6, N.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.9 NAG.9: 3 residues within 4Å: Chain A: I.156, R.157, N.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.156 NAG.10: 1 residues within 4Å: Chain B: N.441 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain B: P.417, V.419, N.420 No protein-ligand interaction detected (PLIP)

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Spike glycoprotein

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