SMTL ID : 8opm.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

12 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: 5 residues within 4Å: Chain A: N.1226 Chain B: D.893, V.894, D.895, N.896 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.893, B:N.896, B:N.896 NAG-NAG.3: 2 residues within 4Å: Chain A: N.40, L.99 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.939 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.697 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain B: N.1226 Chain C: D.893, V.894, D.895, N.896 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.893, C:N.896, C:N.896 NAG-NAG.15: 2 residues within 4Å: Chain B: N.40, L.99 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain B: N.939 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain B: N.697 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 6 residues within 4Å: Chain A: D.893, V.894, D.895, N.896, Q.1016 Chain C: N.1226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.893, A:N.896, A:N.896 NAG-NAG.27: 2 residues within 4Å: Chain C: N.40, L.99 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 1 residues within 4Å: Chain C: N.939 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 1 residues within 4Å: Chain C: N.697 No protein-ligand interaction detected (PLIP)

21 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.2: 9 residues within 4Å: Chain A: D.28, F.29, N.30, I.142, N.143 Chain C: Y.450, S.453, R.457 Ligands: NAG.41 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.30, A:N.30 NAG-NAG-BMA.4: 3 residues within 4Å: Chain A: H.153, E.158, N.199 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 2 residues within 4Å: Chain A: V.675, N.677 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain A: N.203, S.205, T.206 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 3 residues within 4Å: Chain A: N.69, D.283, R.947 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 6 residues within 4Å: Chain A: F.725, D.726, S.727, N.737, T.739, D.740 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.740 NAG-NAG-BMA.11: 2 residues within 4Å: Chain A: F.347, N.444 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 8 residues within 4Å: Chain A: Y.450, R.457 Chain B: D.28, F.29, N.30, I.142, N.143 Ligands: NAG.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.30, B:N.30 NAG-NAG-BMA.16: 3 residues within 4Å: Chain B: H.153, E.158, N.199 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 2 residues within 4Å: Chain B: V.675, N.677 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 3 residues within 4Å: Chain B: N.203, S.205, T.206 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 3 residues within 4Å: Chain B: N.69, D.283, R.947 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 5 residues within 4Å: Chain B: F.725, D.726, N.737, T.739, D.740 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.740 NAG-NAG-BMA.23: 2 residues within 4Å: Chain B: F.347, N.444 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 9 residues within 4Å: Chain B: Y.450, S.453, R.457 Chain C: D.28, F.29, N.30, I.142, N.143 Ligands: NAG.61 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.30, C:N.30 NAG-NAG-BMA.28: 4 residues within 4Å: Chain C: H.153, E.158, K.175, N.199 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 3 residues within 4Å: Chain C: S.656, V.675, N.677 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 3 residues within 4Å: Chain C: N.203, S.205, T.206 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.32: 3 residues within 4Å: Chain C: N.69, D.283, R.947 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.34: 6 residues within 4Å: Chain C: F.725, D.726, S.727, N.737, T.739, D.740 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.740 NAG-NAG-BMA.35: 2 residues within 4Å: Chain C: F.347, N.444 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-5N6.12: 10 residues within 4Å: Chain A: N.37, L.39, T.41, T.93, T.94, K.95, L.96, S.97, S.257, N.259 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.37, A:T.93, A:S.257, A:N.259 Salt bridges: A:K.91, A:K.95, A:K.95 SIA-5N6.24: 11 residues within 4Å: Chain B: N.37, L.39, T.41, I.43, T.93, T.94, K.95, L.96, S.97, S.257, N.259 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.95 Hydrogen bonds: B:N.37, B:T.93, B:S.257, B:N.259 Salt bridges: B:K.91, B:K.95, B:K.95 SIA-5N6.36: 10 residues within 4Å: Chain C: N.37, L.39, T.41, T.93, T.94, K.95, L.96, S.97, W.100, S.257 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.37, C:T.93, C:S.257 Salt bridges: C:K.91, C:K.95, C:K.95

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

NAG.37: 3 residues within 4Å: Chain A: D.630, N.715, N.716 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: N.808, I.1166 Ligand excluded by PLIP NAG.39: 8 residues within 4Å: Chain A: D.337, N.364, N.366, N.618, D.619 Chain C: A.538, Y.539, P.541 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: R.181, N.182 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain A: N.30, N.33 Ligands: NAG-NAG-BMA.2 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain A: N.481, F.484, C.544, S.545, K.547 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain A: N.465 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain A: L.570, S.573, N.575 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain A: S.742, V.743, S.744, E.783, N.786 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain A: N.791 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: D.630, N.715, N.716 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: N.808, I.1166 Ligand excluded by PLIP NAG.49: 8 residues within 4Å: Chain A: A.538, Y.539, P.541 Chain B: D.337, N.364, N.366, N.618, D.619 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain B: R.181, N.182 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain B: N.30, N.33 Ligands: NAG-NAG-BMA.14 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain B: N.481, F.484, C.544, S.545, K.547 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain B: N.465 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain B: V.569, L.570, S.573, N.575 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain B: S.742, V.743, S.744, E.783, N.786 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain B: N.791 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain C: D.630, N.715, N.716 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain C: N.808, I.1166 Ligand excluded by PLIP NAG.59: 7 residues within 4Å: Chain B: A.538, Y.539 Chain C: D.337, N.364, N.366, N.618, D.619 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain C: R.181, N.182 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain C: N.30, N.33 Ligands: NAG-NAG-BMA.26 Ligand excluded by PLIP NAG.62: 5 residues within 4Å: Chain C: N.481, F.484, C.544, S.545, K.547 Ligand excluded by PLIP NAG.63: 1 residues within 4Å: Chain C: N.465 Ligand excluded by PLIP NAG.64: 4 residues within 4Å: Chain C: V.569, L.570, S.573, N.575 Ligand excluded by PLIP NAG.65: 5 residues within 4Å: Chain C: S.742, V.743, S.744, E.783, N.786 Ligand excluded by PLIP NAG.66: 1 residues within 4Å: Chain C: N.791 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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