SMTL ID : 9kr8.1

Overall structure of HKU5 S protein in closed conformation

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: 6 residues within 4Å: Chain A: L.173, N.174 Chain B: S.534, S.537, R.538, D.549 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.538 NAG-NAG.2: 5 residues within 4Å: Chain A: H.189, E.230, K.237, R.248, N.250 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.230 Hydrogen bonds: A:K.237 NAG-NAG.3: 4 residues within 4Å: Chain A: N.418, T.420, K.421, M.585 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.782 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: L.862, N.867, T.869, M.870 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: L.767, H.1143, N.1145 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: N.1172, T.1174, Y.1186, P.1195 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: T.773, V.1210, F.1212, N.1214 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain B: L.173, N.174 Chain C: S.534, S.537, R.538, D.549 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.538 NAG-NAG.10: 5 residues within 4Å: Chain B: E.230, L.233, K.237, R.248, N.250 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.233 Hydrogen bonds: B:K.237 NAG-NAG.11: 4 residues within 4Å: Chain B: N.418, T.420, K.421, M.585 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.782 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: L.862, N.867, T.869 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: H.1143, N.1145 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: N.1172, T.1174, Y.1186, P.1195 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain B: V.1210, F.1212, E.1213, N.1214 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain A: S.534, S.537, R.538, D.549 Chain C: L.173, N.174 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.538 NAG-NAG.18: 4 residues within 4Å: Chain C: L.233, K.237, R.248, N.250 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.233 NAG-NAG.19: 4 residues within 4Å: Chain C: N.418, T.420, K.421, M.585 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain C: N.782 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: L.862, N.867, T.869 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: L.767, H.1143, N.1145 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain C: N.1172, T.1174, Y.1186, P.1195 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain C: T.773, V.1210, F.1212, N.1214 No protein-ligand interaction detected (PLIP)

3 x PLM: PALMITIC ACID(Non-covalent)

PLM.25: 14 residues within 4Å: Chain A: T.400, P.401, P.402, P.403, I.404, A.455, Y.456, S.457, M.460, P.502, N.504, Y.505, A.506, Y.559 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.402, A:I.404, A:A.455, A:P.502, A:P.502 Hydrogen bonds: A:S.457, A:Y.559 PLM.39: 15 residues within 4Å: Chain B: T.400, P.401, P.402, P.403, I.404, K.408, A.455, Y.456, S.457, M.460, P.502, N.504, Y.505, A.506, Y.559 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.403, B:A.455, B:Y.456, B:P.502, B:Y.505, B:Y.505, B:A.506 Hydrogen bonds: B:S.457, B:Y.559 PLM.52: 15 residues within 4Å: Chain C: T.400, P.401, P.402, P.403, I.404, A.455, Y.456, S.457, M.460, P.502, N.504, Y.505, A.506, Y.507, Y.559 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:T.400, C:P.402, C:P.403, C:I.404, C:A.455, C:P.502, C:P.502, C:Y.505, C:Y.505, C:Y.507 Hydrogen bonds: C:S.457, C:Y.559

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

NAG.26: 2 residues within 4Å: Chain A: N.73, V.337 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: P.41, E.45, N.111, Q.115 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.132 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.167 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: V.194, I.243, N.244 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: Q.494, N.495 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.590 Chain B: Y.517 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: E.595, N.617, C.618 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: L.704, N.716 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.760 Chain C: Y.939 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.771 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: N.73, V.337, S.916 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: P.41, N.111, Q.115 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.132, N.258 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.167 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: V.194, I.243, N.244 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: Q.494, N.495 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain B: N.590 Chain C: Y.517 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: N.617, C.618 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: L.704, N.716 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain A: Y.939 Chain B: N.760 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain B: N.771 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: N.73, V.337 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: N.111, Q.115 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.132 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain C: N.167 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain C: I.243, N.244 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain C: Q.494, N.495 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain A: Y.517 Chain C: N.590 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain C: N.617 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain C: L.704, N.716 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain B: Y.939 Chain C: N.760 Ligand excluded by PLIP NAG.63: 1 residues within 4Å: Chain C: N.771 Ligand excluded by PLIP

3 x OLA: OLEIC ACID(Non-covalent)

OLA.37: 14 residues within 4Å: Chain A: Y.463, S.468, A.469 Chain C: F.393, Y.417, L.419, L.422, F.426, V.428, F.431, P.438, V.488, F.569, I.571 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.393, C:Y.417, C:L.419, C:L.422, C:F.426, C:V.428, C:F.431, C:P.438, C:V.488, C:F.569, C:F.569, C:I.571 Hydrogen bonds: A:A.469 OLA.38: 16 residues within 4Å: Chain A: F.393, M.396, Y.417, L.419, L.422, L.423, F.426, V.428, F.431, P.438, L.449, V.451, F.569, I.571 Chain B: S.468, A.469 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.393, A:L.419, A:L.422, A:L.423, A:F.426, A:V.428, A:P.438, A:L.449, A:V.451, A:F.569, A:F.569, A:F.569, A:I.571 Hydrogen bonds: B:A.469 OLA.51: 15 residues within 4Å: Chain B: F.393, Y.417, L.419, L.422, F.426, F.431, P.438, V.451, V.488, F.569, I.571 Chain C: S.462, S.468, A.469, G.470 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.393, B:Y.417, B:L.419, B:L.422, B:F.426, B:P.438, B:V.451, B:V.488, B:V.488, B:F.569, B:F.569 Hydrogen bonds: C:A.469, C:G.470

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y.Y. et al., Molecular Insights into Species-Specific ACE2 Recognition of Coronavirus HKU5. To Be Published

Release Date

2025-11-05

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

Related Entries With Identical Sequence