SMTL ID : 8y8g.1

Structure of HCoV-HKU1C spike in the glycan-activated-1up conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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.1: 2 residues within 4Å: Chain A: I.132, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.322 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: D.701, N.712, T.714 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: D.4, F.5, N.119 No protein-ligand interaction detected (PLIP)

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: 5 residues within 4Å: Chain A: D.4, F.5, N.119, D.164 Chain B: S.551 No protein-ligand interaction detected (PLIP)

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

NAG.6: 3 residues within 4Å: Chain A: N.179, S.181, V.203 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: L.649, N.651 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.689, N.690 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: D.701, N.712, T.714 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.780 Ligand excluded by PLIP NAG.11: 6 residues within 4Å: Chain A: D.313, N.342, S.344, T.345, N.592 Chain B: Y.515 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: V.1197, N.1198 Chain C: D.867, N.868 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.6, C.7, T.8, N.9 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: E.134, N.175 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: N.179, S.181 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.318, N.322 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: L.649, N.651 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.780 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.342, S.344, D.593 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: D.867, P.967 Chain B: V.1197, N.1198 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.45, E.259 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: N.179, S.181, D.183 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: T.650, N.651 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain C: F.700, D.701, N.712, T.714, S.715 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.780 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
C

B
A

C
B

Spike glycoprotein

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