SMTL ID : 8whw.1

Spike Trimer of BA.2.86 with single RBD up

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

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: N.281 Chain B: K.556 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.281 NAG-BMA.3: 1 residues within 4Å: Chain A: 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.715, A:Q.924, A:Q.1069 NAG-BMA.6: 4 residues within 4Å: Chain A: N.1096, T.1098, H.1099, F.1101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.1098 NAG-BMA.7: 2 residues within 4Å: Chain B: N.279, N.281 No protein-ligand interaction detected (PLIP) NAG-BMA.8: 1 residues within 4Å: Chain B: 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.799, B:S.801, B:Q.802 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.1098 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: 2 residues within 4Å: Chain A: K.556 Chain C: N.281 No protein-ligand interaction detected (PLIP) NAG-BMA.14: 1 residues within 4Å: Chain C: N.1132 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1132 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: 3 residues within 4Å: Chain C: N.715, Q.924, Q.1069 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.715 NAG-BMA.17: 4 residues within 4Å: Chain C: N.1096, T.1098, H.1099, F.1101 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.1098

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

NAG.18: 4 residues within 4Å: Chain A: N.123, A.124, T.125, N.126 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: F.341, N.342, F.370 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.330, Q.578 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.614, T.616, E.617 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.655 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: S.706, N.707 Chain C: Y.794 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: A.704, E.1070, K.1071, N.1072 Chain C: Q.893 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: Y.31, T.32, N.33, 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, F.62, N.64 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: S.113, E.133, N.164, N.165 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: T.109, N.233, T.235 Chain C: E.464 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.330, Q.578, T.579 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.614, T.616 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.655 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: Y.794 Chain B: S.706, N.707 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain A: Q.893 Chain B: A.704, E.1070, N.1072 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain B: E.339, R.345, A.347, N.353, T.355 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: H.338, F.341, N.342, F.370 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain C: N.123, A.124, T.125, N.126, V.171 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: Y.31, F.62, N.64 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.614, T.616 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.655 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain B: I.792, Y.794 Chain C: S.706, N.707 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain B: Q.893 Chain C: A.704, E.1070, K.1071, N.1072 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.342, T.344 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain A: E.464 Chain C: T.109, N.233, T.235 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: N.330, P.577, Q.578 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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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