SMTL ID : 8xus.1

JN.1 Spike Trimer in complex with heparan sulfate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.123, T.125, N.126, V.127, V.171 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: E.133, N.164, N.165 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Chain A: N.233 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.244 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.279, E.280, N.281 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.330, Q.578, L.580 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: H.338, N.342, A.343, F.370 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.353, T.355 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.614, Q.642 Chain C: K.833, Y.835 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.655 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.707 Chain C: Y.794 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.715, Q.924, Q.1069 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: K.793, N.799, F.800, S.801 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: A.704, A.711, E.1070, K.1071, N.1072 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: N.1096, G.1097, T.1098, H.1099, F.1101 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.1132 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: Y.31, N.64 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.601 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain B: N.123, T.125, N.126, V.127, V.171 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.233 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.244 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.279, E.280, N.281 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.330, Q.578, L.580 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: H.338, N.342, A.343, F.370 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.353, T.355 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: Y.835, G.836 Chain B: N.614 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.655 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: Y.794 Chain B: N.707 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.715, Q.924, Q.1069 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: K.793, N.799, S.801 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain B: A.704, A.711, E.1070, K.1071, N.1072 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain B: N.1096, G.1097, T.1098, H.1099, F.1101 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.1132 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: Y.31, N.64 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.601 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain C: N.123, T.125, N.126, V.127, F.128, V.171 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.233 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.244 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.279, E.280, N.281 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.330, Q.578, L.580 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: H.338, N.342, A.343, F.370 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.353, T.355 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: K.833 Chain C: N.614, Q.642 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.655 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: Y.794 Chain C: N.707 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: N.715, Q.924, Q.1069 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: K.793, N.799, S.801 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain C: A.704, A.711, E.1070, K.1071, N.1072 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain C: N.1096, G.1097, T.1098, H.1099, F.1101 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.1132 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.601 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain C: Y.31, F.62, S.63, N.64 Ligand excluded by PLIP

1 x IDU: 2-O-sulfo-beta-L-altropyranuronic acid(Non-covalent)

IDU.53: 6 residues within 4Å: Chain A: R.354, T.355, R.356 Chain C: T.167, F.168, E.169 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:F.168, C:E.169, C:E.169, A:R.356

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
C

B
A

C
B

Spike glycoprotein

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