SMTL ID : 8y7y.1

Local structure of HCoV-HKU1A spike in complex with TMPRSS2 and glycan

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-mer

Ligands

2 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: H.129, V.132, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.2: 5 residues within 4Å: Chain A: D.4, F.5, N.119, T.141 Ligands: NAG.9 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.3: 3 residues within 4Å: Chain A: N.179, S.181, T.182 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 5 residues within 4Å: Chain C: N.342, S.344, T.345, N.594, P.599 No protein-ligand interaction detected (PLIP)

4 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: F.10, N.158 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: T.236, N.238 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: V.651, N.653 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain C: I.419, N.420 No protein-ligand interaction detected (PLIP)

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

NAG.9: 3 residues within 4Å: Chain A: N.6, N.9 Ligands: NAG-NAG-BMA-MAN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.6, A:N.9 NAG.10: 2 residues within 4Å: Chain A: N.16, L.75 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.75 NAG.12: 1 residues within 4Å: Chain C: N.441 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.441 NAG.13: 2 residues within 4Å: Chain C: S.549, N.551 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.11: 11 residues within 4Å: Chain A: N.13, L.15, T.17, T.18, L.66, K.67, T.69, Y.71, S.73, W.76, S.233 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.66, A:Y.71, A:W.76 Hydrogen bonds: A:N.13, A:T.17, A:K.67 Salt bridges: A:K.67

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: AC
Transmembrane protease serine 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
T

Spike glycoprotein

Transmembrane protease serine 2

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