SMTL ID : 9eh8.1

Structure of the prefusion HKU5-19s Spike trimer (conformation 2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.00 Å

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- NAG: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-NAG.1: 15 residues within 4Å: Chain A: Q.742, S.743, L.744, L.771, N.772 Chain B: E.892, R.893, K.894, Y.895, D.911, Y.914, M.915, D.949, P.950, Y.951 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.951, B:R.893, B:E.892 NAG-NAG-BMA-MAN-MAN-MAN-MAN-NAG.14: 15 residues within 4Å: Chain B: Q.742, S.743, L.744, L.771, N.772 Chain C: E.892, R.893, K.894, Y.895, D.911, Y.914, M.915, D.949, P.950, Y.951 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.951, C:R.893, C:E.892 NAG-NAG-BMA-MAN-MAN-MAN-MAN-NAG.27: 15 residues within 4Å: Chain A: E.892, R.893, K.894, Y.895, D.911, Y.914, M.915, D.949, P.950, Y.951 Chain C: Q.742, S.743, L.744, L.771, N.772 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.951, A:R.893, A:E.892

27 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: P.52, N.122, R.125 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.173, N.178 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.794 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: L.874, N.879, M.882 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: N.1184, Y.1198 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: T.785, V.1222, K.1223, F.1224, N.1226 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain A: L.716, N.728 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: N.185 Chain C: S.549, R.550 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain A: I.205, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: P.52, N.122, R.125 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain B: N.173, N.178 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain B: N.794 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain B: L.874, N.879, M.882 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain B: N.1184, Y.1198 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain B: T.785, V.1222, K.1223, F.1224, N.1226 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain B: L.716, N.728 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain A: S.549, R.550 Chain B: N.185 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain B: I.205, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain C: P.52, N.122, R.125 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 2 residues within 4Å: Chain C: N.173, N.178 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 1 residues within 4Å: Chain C: N.794 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain C: L.874, N.879, M.882 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 2 residues within 4Å: Chain C: N.1184, Y.1198 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 5 residues within 4Å: Chain C: T.785, V.1222, K.1223, F.1224, N.1226 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 2 residues within 4Å: Chain C: L.716, N.728 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain B: S.549, R.550 Chain C: N.185 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 2 residues within 4Å: Chain C: I.205, N.256 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.4: 7 residues within 4Å: Chain A: D.36, G.38, L.198, H.200, L.242, R.260, N.262 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.260 NAG-NAG-BMA-MAN-MAN.17: 7 residues within 4Å: Chain B: D.36, G.38, L.198, H.200, L.242, R.260, N.262 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.260 NAG-NAG-BMA-MAN-MAN.30: 7 residues within 4Å: Chain C: D.36, G.38, L.198, H.200, L.242, R.260, N.262 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.260

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.5: 4 residues within 4Å: Chain A: N.430, K.433, M.597 Chain C: K.531 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.18: 4 residues within 4Å: Chain A: K.531 Chain B: N.430, K.433, M.597 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.31: 4 residues within 4Å: Chain B: K.531 Chain C: N.430, K.433, M.597 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.13: 6 residues within 4Å: Chain A: G.139, A.142, N.143, E.269, N.270, F.294 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.270 NAG-NAG-BMA.26: 6 residues within 4Å: Chain B: G.139, A.142, N.143, E.269, N.270, F.294 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.270 NAG-NAG-BMA.39: 6 residues within 4Å: Chain C: G.139, A.142, N.143, E.269, N.270, F.294 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.270

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

NAG.40: 2 residues within 4Å: Chain A: P.176, N.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.176, A:N.178 NAG.41: 2 residues within 4Å: Chain A: N.84, V.349 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.349 Hydrogen bonds: A:N.84 NAG.42: 5 residues within 4Å: Chain A: T.778, L.779, A.780, H.1155, N.1157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.780 NAG.43: 1 residues within 4Å: Chain A: N.629 1 PLIP interactions: 1 interactions with chain A Water bridges: A:C.630 NAG.44: 1 residues within 4Å: Chain A: N.602 No protein-ligand interaction detected (PLIP) NAG.47: 2 residues within 4Å: Chain B: P.176, N.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.176, B:N.178 NAG.48: 2 residues within 4Å: Chain B: N.84, V.349 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.349 Hydrogen bonds: B:N.84 NAG.49: 5 residues within 4Å: Chain B: T.778, L.779, A.780, H.1155, N.1157 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.780 NAG.50: 1 residues within 4Å: Chain B: N.629 1 PLIP interactions: 1 interactions with chain B Water bridges: B:C.630 NAG.51: 1 residues within 4Å: Chain B: N.602 No protein-ligand interaction detected (PLIP) NAG.55: 2 residues within 4Å: Chain C: P.176, N.178 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.176, C:N.178 NAG.56: 2 residues within 4Å: Chain C: N.84, V.349 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.349 Hydrogen bonds: C:N.84 NAG.57: 5 residues within 4Å: Chain C: T.778, L.779, A.780, H.1155, N.1157 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.780 NAG.58: 1 residues within 4Å: Chain C: N.629 1 PLIP interactions: 1 interactions with chain C Water bridges: C:C.630 NAG.59: 1 residues within 4Å: Chain C: N.602 No protein-ligand interaction detected (PLIP)

3 x FOL: FOLIC ACID(Non-covalent)

FOL.45: 11 residues within 4Å: Chain A: W.62, L.64, A.141, K.144, G.146, T.147, I.158, A.329, W.330, A.331, A.332 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.141 Hydrogen bonds: A:T.147, A:T.147, A:T.147, A:W.330, A:A.332 Water bridges: A:A.141 pi-Stacking: A:W.62, A:W.62, A:W.62 pi-Cation interactions: A:K.144 FOL.52: 11 residues within 4Å: Chain B: W.62, L.64, A.141, K.144, G.146, T.147, I.158, A.329, W.330, A.331, A.332 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.141 Hydrogen bonds: B:T.147, B:T.147, B:T.147, B:W.330, B:A.332 Water bridges: B:A.141 pi-Stacking: B:W.62, B:W.62, B:W.62 pi-Cation interactions: B:K.144 FOL.60: 11 residues within 4Å: Chain C: W.62, L.64, A.141, K.144, G.146, T.147, I.158, A.329, W.330, A.331, A.332 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.141 Hydrogen bonds: C:T.147, C:T.147, C:T.147, C:W.330, C:A.332 Water bridges: C:A.141 pi-Stacking: C:W.62, C:W.62, C:W.62 pi-Cation interactions: C:K.144

3 x EIC: LINOLEIC ACID(Non-covalent)

EIC.46: 16 residues within 4Å: Chain A: Y.475, S.480, A.481, G.482 Chain B: F.405, M.408, Y.429, L.431, F.438, V.440, F.443, P.450, L.453, L.461, F.581, I.583 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.405, B:Y.429, B:L.431, B:F.438, B:V.440, B:F.443, B:L.453, B:L.461, B:F.581, B:F.581, B:I.583 Hydrogen bonds: A:A.481, A:G.482 Water bridges: A:S.480 EIC.53: 16 residues within 4Å: Chain B: Y.475, S.480, A.481, G.482 Chain C: F.405, M.408, Y.429, L.431, F.438, V.440, F.443, P.450, L.453, L.461, F.581, I.583 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.405, C:Y.429, C:L.431, C:F.438, C:V.440, C:F.443, C:L.453, C:L.461, C:F.581, C:F.581, C:I.583 Hydrogen bonds: B:A.481, B:G.482 Water bridges: B:S.480 EIC.54: 16 residues within 4Å: Chain A: F.405, M.408, Y.429, L.431, F.438, V.440, F.443, P.450, L.453, L.461, F.581, I.583 Chain C: Y.475, S.480, A.481, G.482 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.405, A:Y.429, A:L.431, A:F.438, A:V.440, A:F.443, A:L.453, A:L.461, A:F.581, A:F.581, A:I.583 Hydrogen bonds: C:A.481, C:G.482 Water bridges: C:S.480

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, Y.J. et al., Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses. Cell (2025)

Release Date

2025-02-26

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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