- Coordinates
- PDB Format
- 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
- 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
AB
BC
C
- Coordinates
- PDB Format
- 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
- 30 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 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
- 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
- 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
- 9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 6 x ZN: ZINC ION(Non-covalent)
- 3 x FOL: FOLIC ACID(Non-covalent)
- 3 x EIC: LINOLEIC ACID(Non-covalent)
- 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
AB
BC
C