SMTL ID : 8opo.1

Human Coronavirus HKU1 spike glycoprotein in complex with an alpha2,8-linked 9-O-acetylated disialoside (3-up state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

9 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: 3 residues within 4Å: Chain A: N.203, S.205, T.206 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.40, P.44 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.69, D.283, R.947 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.203, S.205, T.206 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.40, P.44 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.69, D.283, R.947 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: N.203, S.205, T.206 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain C: N.40, P.44 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.69, D.283, R.947 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-5N6.10: 8 residues within 4Å: Chain A: N.37, L.39, T.41, I.43, K.91, T.93, K.95, S.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.93, A:T.93, A:T.93, A:N.259 Salt bridges: A:K.91, A:K.95, A:K.95 SIA-5N6.11: 8 residues within 4Å: Chain B: N.37, T.41, I.43, K.91, T.93, K.95, W.100, S.257 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.100 Hydrogen bonds: B:T.41, B:T.93, B:T.93, B:T.93, B:N.259 Salt bridges: B:K.91, B:K.95, B:K.95 SIA-5N6.12: 9 residues within 4Å: Chain C: N.37, L.39, T.41, I.43, K.91, T.93, K.95, S.257, N.259 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.93, C:T.93, C:T.93 Salt bridges: C:K.91, C:K.95, C:K.95

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

NAG.13: 1 residues within 4Å: Chain A: N.677 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: H.695, N.697 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.737 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.808 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: S.796, N.1226 Chain B: N.896, K.1017 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: F.347, I.443, N.444 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.30, N.33 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: S.179, S.180, R.181, N.182 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: V.156, E.158, N.199 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.143, T.165 Ligand excluded by PLIP NAG.23: 8 residues within 4Å: Chain A: R.331, D.334, N.364, F.365, N.366, N.618, Q.622, N.624 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.677 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: H.695, N.697 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.737 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.808 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: S.796, N.1226 Chain C: N.896, K.1017 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: F.347, I.443, N.444 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.30, N.33 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: S.179, S.180, R.181, N.182 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: V.156, E.158, N.199 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.143, T.165 Ligand excluded by PLIP NAG.34: 8 residues within 4Å: Chain B: R.331, D.334, N.364, F.365, N.366, N.618, Q.622, N.624 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.677 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: H.695, N.697 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.737 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.808 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain A: D.895, N.896, K.1017 Chain C: S.796, N.1226 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: F.347, I.443, N.444 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.30, N.33 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: S.179, S.180, R.181, N.182 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: V.156, E.158, N.199 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.143, T.165 Ligand excluded by PLIP NAG.45: 8 residues within 4Å: Chain C: R.331, D.334, N.364, F.365, N.366, N.618, Q.622, N.624 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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