SMTL ID : 8opn.1

Human Coronavirus HKU1 spike glycoprotein in complex with an alpha2,8-linked 9-O-acetylated disialoside (1-up state)

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: 4 residues within 4Å: Chain A: N.1226 Chain B: V.894, D.895, N.896 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.895, B:N.896, B:N.896, B:N.896 NAG-NAG.2: 1 residues within 4Å: Chain B: N.69 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: D.893, V.894, D.895, N.896, S.995 Chain C: N.1226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.893, A:D.895, A:N.896 NAG-NAG.4: 2 residues within 4Å: Chain C: N.69, D.283 No protein-ligand interaction detected (PLIP)

3 x SIA- 5N6: 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-8)-N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA-5N6.5: 11 residues within 4Å: Chain A: N.37, L.39, T.41, K.91, T.93, T.94, K.95, N.254, A.255, S.257, N.259 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.95 Hydrogen bonds: A:N.37, A:T.93, A:T.93, A:T.93, A:K.91, A:K.91 Salt bridges: A:K.91, A:K.95, A:K.95 SIA-5N6.6: 13 residues within 4Å: Chain B: N.37, L.39, T.41, K.91, T.93, K.95, L.96, S.97, W.100, S.257, S.258, N.259, T.260 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.95, B:W.100 Hydrogen bonds: B:N.37, B:T.93, B:T.93, B:T.93, B:S.257, B:S.257, B:N.259, B:T.260 Salt bridges: B:K.91, B:K.95, B:K.95 SIA-5N6.7: 10 residues within 4Å: Chain C: N.37, T.41, K.91, T.93, K.95, W.100, N.254, S.257, N.259, T.260 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.95, C:W.100 Hydrogen bonds: C:N.37, C:T.93, C:T.93, C:T.93, C:S.257, C:S.257, C:N.259, C:T.260 Salt bridges: C:K.91, C:K.95, C:K.95

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

NAG.8: 3 residues within 4Å: Chain A: H.153, E.158, N.199 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: F.674, V.675, N.677 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: F.725, D.726, N.737, T.739 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.808, I.1166 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.203, S.205, T.206 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: H.695, N.697 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.69, D.283 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: S.744, N.786 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.808, I.1166 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: F.347, I.443, N.444 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: H.695, N.697 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: D.726, N.737, L.738, T.739 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.1226 Chain C: D.895, N.896, S.995 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: F.674, V.675, T.676, N.677 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: E.935, N.939, E.945 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: H.153, E.158, N.199 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.203, S.205, T.206 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: F.34, S.180, R.181, N.182 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.40, L.99 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: N.203, S.205, T.206, S.227 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: V.675, N.677 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.808, I.1166 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain B: R.542 Chain C: D.337, N.366, N.618, D.619, L.621 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: H.695, N.697 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: F.725, D.726, N.737, T.739 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: H.153, E.158, K.175, N.199 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pronker, M.F. et al., Sialoglycan binding triggers spike opening in a human coronavirus. Nature (2023)

Release Date

2023-08-02

Peptides

Spike glycoprotein,General control transcription factor GCN4: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,General control transcription factor GCN4

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