SMTL ID : 8whs.1

Spike Trimer of BA.2.86 in complex with one hACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

17 x NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-BMA.1: 4 residues within 4Å: Chain A: E.339, N.353, R.354, T.355 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.354 NAG-BMA.2: 2 residues within 4Å: Chain A: E.280, N.281 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.280, A:N.281 NAG-BMA.3: 2 residues within 4Å: Chain A: I.1130, N.1132 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1132 NAG-BMA.4: 3 residues within 4Å: Chain A: N.799, S.801, Q.802 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.799, A:S.801, A:Q.802 NAG-BMA.5: 4 residues within 4Å: Chain A: N.715, L.920, Q.924, Q.1069 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.924, A:Q.1069 NAG-BMA.6: 3 residues within 4Å: Chain A: N.1096, H.1099, F.1101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.1099 NAG-BMA.7: 3 residues within 4Å: Chain B: N.279, E.280, N.281 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.279, B:E.280, B:E.280 NAG-BMA.8: 2 residues within 4Å: Chain B: I.1130, N.1132 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1132 NAG-BMA.9: 3 residues within 4Å: Chain B: N.799, S.801, Q.802 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.801 NAG-BMA.10: 4 residues within 4Å: Chain B: N.715, L.920, Q.924, Q.1069 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.715 NAG-BMA.11: 4 residues within 4Å: Chain B: N.1096, T.1098, H.1099, F.1101 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.1098 Hydrogen bonds: B:T.1098, B:H.1099 NAG-BMA.12: 3 residues within 4Å: Chain C: E.339, N.353, T.355 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.339 NAG-BMA.13: 3 residues within 4Å: Chain C: N.279, E.280, N.281 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.279, C:E.280, C:E.280 NAG-BMA.14: 2 residues within 4Å: Chain C: I.1130, N.1132 No protein-ligand interaction detected (PLIP) NAG-BMA.15: 3 residues within 4Å: Chain C: N.799, S.801, Q.802 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.799, C:S.801 NAG-BMA.16: 2 residues within 4Å: Chain C: N.715, Q.1069 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.715, C:Q.1069 NAG-BMA.17: 3 residues within 4Å: Chain C: N.1096, H.1099, F.1101 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1099

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

NAG.18: 5 residues within 4Å: Chain A: N.123, A.124, T.125, N.126, F.128 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.342, F.370 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.330, Q.578, L.580 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain A: N.614, T.616 Chain C: I.832, K.833, Y.835 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: Y.653, N.655 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.707 Chain C: I.792, Y.794 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: A.704, E.1070, K.1071, N.1072 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: Y.31, N.64 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: G.231, N.233 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain B: N.123, T.125, N.126, V.127, F.128, V.171 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: Y.31, S.63, N.64 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.353, R.354 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.342, F.370 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: N.233 Chain C: E.464, R.465, D.466 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: N.330, Q.578, T.579, L.580 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain A: K.833, Q.834, Y.835, G.836 Chain B: N.614 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: Y.653, N.655 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: I.792, Y.794 Chain B: S.706, N.707 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: A.704, E.1070, N.1072 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain C: N.123, A.124, T.125, N.126, V.127, V.171 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: Y.31, F.62, S.63, N.64 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain A: K.461, E.464 Chain C: N.233, T.235 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.614, T.616 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: Y.653, N.655 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: Y.794 Chain C: S.706, N.707 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: A.704, E.1070, K.1071, N.1072 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.342, T.344, F.370 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: R.327, P.329, N.330, V.331 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain D: K.398, S.527, N.528 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain D: K.8, N.72, T.74 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain D: K.291, V.298, N.304 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain D: N.35, Q.322 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.49: 4 residues within 4Å: Chain D: H.356, E.357, H.360, E.384 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.356, D:H.360, D:E.384

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.50: 3 residues within 4Å: Chain D: R.151, W.253, F.434 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, P. et al., Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity. Natl Sci Rev (2024)

Release Date

2024-07-03

Peptides

Spike glycoprotein: ABC
Processed angiotensin-converting enzyme 2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Spike glycoprotein

Processed angiotensin-converting enzyme 2

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