SMTL ID : 9ea0.1

Structure of the prefusion HKU5-19s Spike trimer (conformation 1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.00 Å

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- NAG: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-NAG.1: 14 residues within 4Å: Chain A: Q.742, L.744, T.770, N.772 Chain B: E.892, R.893, Y.895, D.911, Y.914, M.915, D.949, P.950, Y.951 Ligands: NAG-NAG.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.951, B:R.893 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-NAG.15: 14 residues within 4Å: Chain B: Q.742, L.744, T.770, N.772 Chain C: E.892, R.893, Y.895, D.911, Y.914, M.915, D.949, P.950, Y.951 Ligands: NAG-NAG.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.951, C:R.893 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-NAG.29: 14 residues within 4Å: Chain A: E.892, R.893, Y.895, D.911, Y.914, M.915, D.949, P.950, Y.951 Chain C: Q.742, L.744, T.770, N.772 Ligands: NAG-NAG.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.951, A:R.893

30 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.4: 3 residues within 4Å: Chain A: N.185 Chain C: S.549, R.550 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: I.205, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: Q.397, T.399, N.602, Y.654 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: N.728, T.729, S.730 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-NAG.1 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain A: N.794 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain A: L.874, N.879, T.881, M.882, Q.1018 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain A: N.1184, Y.1198, P.1207 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain A: V.1222, F.1224, N.1226 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: P.52, N.122, R.125 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain B: N.173, N.178 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain A: S.549, R.550 Chain B: N.185 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain B: I.205, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain B: Q.397, T.399, N.602, Y.654 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain B: N.728, T.729, S.730 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-NAG.15 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 1 residues within 4Å: Chain B: N.794 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain B: L.874, N.879, T.881, M.882, Q.1018 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain B: N.1184, Y.1198, P.1207 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain B: V.1222, F.1224, N.1226 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain C: P.52, N.122, R.125 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 2 residues within 4Å: Chain C: N.173, N.178 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain B: S.549, R.550 Chain C: N.185 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 2 residues within 4Å: Chain C: I.205, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 4 residues within 4Å: Chain C: Q.397, T.399, N.602, Y.654 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 4 residues within 4Å: Chain C: N.728, T.729, S.730 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-NAG.29 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 1 residues within 4Å: Chain C: N.794 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 5 residues within 4Å: Chain C: L.874, N.879, T.881, M.882, Q.1018 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 3 residues within 4Å: Chain C: N.1184, Y.1198, P.1207 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 3 residues within 4Å: Chain C: V.1222, F.1224, N.1226 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.6: 8 residues within 4Å: Chain A: D.36, G.38, T.39, L.198, H.200, L.242, R.260, N.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.36, A:R.260, A:R.260 NAG-NAG-BMA-MAN-MAN.20: 8 residues within 4Å: Chain B: D.36, G.38, T.39, L.198, H.200, L.242, R.260, N.262 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.36, B:R.260, B:R.260 NAG-NAG-BMA-MAN-MAN.34: 8 residues within 4Å: Chain C: D.36, G.38, T.39, L.198, H.200, L.242, R.260, N.262 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.36, C:R.260, C:R.260

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.7: 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.21: 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.35: 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- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.14: 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-FUC.28: 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-FUC.42: 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

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

NAG.43: 4 residues within 4Å: Chain A: N.84, V.349, Q.927, S.928 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.349 Hydrogen bonds: A:N.84, A:S.928, A:A.929 NAG.44: 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.45: 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.50: 4 residues within 4Å: Chain B: N.84, V.349, Q.927, S.928 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.349 Hydrogen bonds: B:N.84, B:S.928, B:A.929 NAG.51: 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.52: 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.58: 4 residues within 4Å: Chain C: N.84, V.349, Q.927, S.928 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.349 Hydrogen bonds: C:N.84, C:S.928, C:A.929 NAG.59: 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.60: 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

6 x ZN: ZINC ION(Non-covalent)

ZN.46: 3 residues within 4Å: Chain A: H.628, H.691, M.695 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.628, A:H.691, H2O.15 ZN.47: 4 residues within 4Å: Chain A: H.284, H.300, A.302, T.303 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.284, A:H.300, A:T.303 ZN.53: 3 residues within 4Å: Chain B: H.628, H.691, M.695 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.628, B:H.691, H2O.30 ZN.54: 4 residues within 4Å: Chain B: H.284, H.300, A.302, T.303 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.284, B:H.300, B:T.303 ZN.61: 3 residues within 4Å: Chain C: H.628, H.691, M.695 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.628, C:H.691, H2O.46 ZN.62: 4 residues within 4Å: Chain C: H.284, H.300, A.302, T.303 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.284, C:H.300, C:T.303

3 x FOL: FOLIC ACID(Non-covalent)

FOL.48: 10 residues within 4Å: Chain A: W.62, L.64, A.141, K.144, G.146, T.147, I.158, W.330, A.331, A.332 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.64, A:L.64, A:A.141 Hydrogen bonds: A:K.144, A:T.147, A:T.147, A:T.147, A:A.332 Water bridges: A:A.141, A:W.330, A:Y.334 pi-Stacking: A:W.62, A:W.62, A:W.62 pi-Cation interactions: A:K.144 FOL.55: 10 residues within 4Å: Chain B: W.62, L.64, A.141, K.144, G.146, T.147, I.158, W.330, A.331, A.332 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.64, B:L.64, B:A.141 Hydrogen bonds: B:K.144, B:T.147, B:T.147, B:T.147, B:A.332 Water bridges: B:A.141, B:W.330, B:Y.334 pi-Stacking: B:W.62, B:W.62, B:W.62 pi-Cation interactions: B:K.144 FOL.63: 10 residues within 4Å: Chain C: W.62, L.64, A.141, K.144, G.146, T.147, I.158, W.330, A.331, A.332 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:L.64, C:L.64, C:A.141 Hydrogen bonds: C:K.144, C:T.147, C:T.147, C:T.147, C:A.332 Water bridges: C:A.141, C:W.330, C:Y.334 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.49: 18 residues within 4Å: Chain A: S.480, A.481, G.482 Chain B: F.405, M.408, L.431, L.434, L.435, F.438, V.440, F.443, P.450, L.453, V.463, V.500, A.502, F.581, I.583 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.405, B:L.431, B:L.431, B:L.434, B:F.438, B:F.438, B:V.440, B:F.443, B:F.443, B:L.453, B:L.453, B:V.463, B:V.500, B:V.500, B:A.502, B:F.581, B:F.581, B:F.581 Hydrogen bonds: A:A.481 EIC.56: 18 residues within 4Å: Chain B: S.480, A.481, G.482 Chain C: F.405, M.408, L.431, L.434, L.435, F.438, V.440, F.443, P.450, L.453, V.463, V.500, A.502, F.581, I.583 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.405, C:L.431, C:L.431, C:L.434, C:F.438, C:F.438, C:V.440, C:F.443, C:F.443, C:L.453, C:L.453, C:V.463, C:V.500, C:V.500, C:A.502, C:F.581, C:F.581, C:F.581 Hydrogen bonds: B:A.481 EIC.57: 18 residues within 4Å: Chain A: F.405, M.408, L.431, L.434, L.435, F.438, V.440, F.443, P.450, L.453, V.463, V.500, A.502, F.581, I.583 Chain C: S.480, A.481, G.482 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.405, A:L.431, A:L.431, A:L.434, A:F.438, A:F.438, A:V.440, A:F.443, A:F.443, A:L.453, A:L.453, A:V.463, A:V.500, A:V.500, A:A.502, A:F.581, A:F.581, A:F.581 Hydrogen bonds: C:A.481

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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