SMTL ID : 8y8f.1

Structure of HCoV-HKU1C spike in the glycan-activated-closed conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 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: 2 residues within 4Å: Chain A: I.132, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.322, R.334 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.334 NAG-NAG.4: 4 residues within 4Å: Chain C: D.4, F.5, V.118, N.119 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.5

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.3: 3 residues within 4Å: Chain A: D.4, N.119, T.141 No protein-ligand interaction detected (PLIP)

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

NAG.5: 2 residues within 4Å: Chain A: N.45, E.259 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain A: D.313, N.342, T.345, N.592 Chain B: Y.515 Ligand excluded by PLIP NAG.7: 5 residues within 4Å: Chain A: G.604, V.605, C.606, N.689, N.690 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.179, S.181 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: S.719, N.758 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: L.649, N.651 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.780 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: D.701, N.712, T.714 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.1198 Chain C: D.867, N.868 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.420 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.6, N.9, Y.145 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain B: G.604, V.605, C.606, I.619, N.690 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: D.701, N.712, T.714 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.780 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: L.649, N.651 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.318, N.322 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.179 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: D.867, N.868, P.967 Chain B: N.1198 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.342, T.345 Chain C: Y.515 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.45 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: D.4, F.5, N.119, T.141 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: V.419, N.420 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.441 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.45 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.179, S.181 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: D.701, N.712 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.175 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain A: Y.515 Chain C: D.313, N.340, N.342, N.592 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: D.867, N.868 Chain C: V.1197, N.1198 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.6, N.9, E.144 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: R.157, N.158 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.318, N.322 Ligand excluded by 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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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