SMTL ID : 8ohn.1

Human Coronavirus HKU1 spike glycoprotein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

24 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: H.153, V.156, E.158, N.199 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: T.629, D.630, N.715, N.716 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.630 NAG-NAG.3: 6 residues within 4Å: Chain A: D.337, N.366, N.618, L.621 Chain C: Y.539, P.541 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.621 NAG-NAG.5: 2 residues within 4Å: Chain A: H.695, N.697 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: D.726, N.737, D.740 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain A: N.1226 Chain B: D.893, V.894, D.895, N.896, Q.1016 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.893, B:D.895, B:N.896 NAG-NAG.8: 3 residues within 4Å: Chain A: N.69, D.283, R.947 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain A: V.675, N.677 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: H.153, V.156, E.158, N.199 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: T.629, D.630, N.715, N.716 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:D.630 NAG-NAG.12: 6 residues within 4Å: Chain A: Y.539, P.541 Chain B: D.337, N.366, N.618, L.621 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.621 NAG-NAG.14: 2 residues within 4Å: Chain B: H.695, N.697 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: D.726, N.737, T.739, D.740 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain B: N.1226 Chain C: D.893, V.894, D.895, N.896, Q.1016 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.893, C:D.895, C:N.896 NAG-NAG.17: 3 residues within 4Å: Chain B: N.69, D.283, R.947 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain B: V.675, N.677 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: H.153, E.158, N.199 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain C: T.629, D.630, N.715, N.716 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:D.630 NAG-NAG.21: 6 residues within 4Å: Chain B: Y.539, P.541 Chain C: D.337, N.366, N.618, L.621 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.621 NAG-NAG.23: 2 residues within 4Å: Chain C: H.695, N.697 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain C: D.726, N.737, D.740 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:D.895, A:N.896 NAG-NAG.26: 3 residues within 4Å: Chain C: N.69, D.283, R.947 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 2 residues within 4Å: Chain C: V.675, N.677 No protein-ligand interaction detected (PLIP)

3 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.4: 4 residues within 4Å: Chain A: D.28, F.29, N.143, T.165 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain B: D.28, F.29, N.143, T.165 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 4 residues within 4Å: Chain C: D.28, F.29, N.143, T.165 No protein-ligand interaction detected (PLIP)

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

NAG.28: 4 residues within 4Å: Chain A: N.30, C.31, T.32, N.33 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: S.180, R.181, N.182 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.203, S.205, T.206 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain A: N.465 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.481 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: S.742, S.744, N.786 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.791 Chain B: N.885 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.808, I.1166 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: E.935, N.939 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.444 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: N.30, C.31, T.32, N.33 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: S.180, R.181, N.182 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: N.203, S.205, T.206 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.465 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.481 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: S.742, S.744, N.786 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: N.791 Chain C: N.885 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: N.808, I.1166 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain B: E.935, N.939 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.444 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: N.30, C.31, T.32, N.33 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: S.180, R.181, N.182 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: N.203, S.205, T.206 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.465 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: N.481, S.545 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: S.742, S.744, N.786 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain A: N.885 Chain C: N.791 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: N.808, I.1166 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: E.935, N.939 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain C: N.444 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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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