SMTL ID : 8x50.1

BA.2.86 Spike Trimer with ins483V mutation (1 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: 3 residues within 4Å: Chain A: E.339, N.353, R.354 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.339, A:N.353 NAG-BMA.2: 3 residues within 4Å: Chain A: E.280, N.281 Chain B: K.557 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.557, B:K.557, A:N.281, A:N.281, A:N.281 NAG-BMA.3: 1 residues within 4Å: Chain A: N.1133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1133 NAG-BMA.4: 3 residues within 4Å: Chain A: N.800, S.802, Q.803 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.800, A:S.802, A:Q.803 NAG-BMA.5: 3 residues within 4Å: Chain A: N.716, Q.925, Q.1070 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.1070 NAG-BMA.6: 4 residues within 4Å: Chain A: N.1097, T.1099, H.1100, F.1102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.1099, A:H.1100 NAG-BMA.7: 3 residues within 4Å: Chain B: N.279, E.280, N.281 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.279, B:E.280 NAG-BMA.8: 1 residues within 4Å: Chain B: N.1133 No protein-ligand interaction detected (PLIP) NAG-BMA.9: 3 residues within 4Å: Chain B: N.800, S.802, Q.803 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.800, B:S.802, B:Q.803 NAG-BMA.10: 4 residues within 4Å: Chain B: N.716, L.921, Q.925, Q.1070 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.716, B:Q.1070 NAG-BMA.11: 4 residues within 4Å: Chain B: N.1097, T.1099, H.1100, F.1102 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.1099 Hydrogen bonds: B:T.1099, B:H.1100 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.557 Chain C: N.281 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.279, C:E.280, A:K.557 NAG-BMA.14: 1 residues within 4Å: Chain C: N.1133 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1133 NAG-BMA.15: 3 residues within 4Å: Chain C: N.800, S.802, Q.803 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.800, C:S.802, C:Q.803 NAG-BMA.16: 3 residues within 4Å: Chain C: N.716, Q.925, Q.1070 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.716, C:Q.1070 NAG-BMA.17: 4 residues within 4Å: Chain C: N.1097, T.1099, H.1100, F.1102 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.1099 Hydrogen bonds: C:T.1099, C:H.1100

31 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: 5 residues within 4Å: Chain A: H.338, F.341, N.342, F.370, W.435 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.330, P.578, Q.579 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.615, T.617, E.618 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: Y.654, N.656 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: S.707, N.708 Chain C: Y.795 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: A.705, E.1071, K.1072, N.1073 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: Y.31, N.33, N.64 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: 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: 5 residues within 4Å: Chain B: N.233, T.235 Chain C: E.464, R.465, D.466 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.330, Q.579 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.615, T.617 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.656 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: Y.795 Chain B: S.707, N.708 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: A.705, E.1071, K.1072, N.1073 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: 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: 6 residues within 4Å: Chain C: N.123, A.124, T.125, N.126, V.127, 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: 5 residues within 4Å: Chain A: K.461, E.464 Chain C: T.109, N.233, T.235 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: N.615, T.617, E.618 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: Y.654, N.656 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain B: I.793, Y.795 Chain C: S.707, N.708 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: A.705, E.1071, K.1072, N.1073 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.342, T.344 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.330 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

2024-06-26

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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