SMTL ID : 8xut.1

XBB.1.5 Spike Trimer in complex with heparan sulfate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: Y.25, N.58 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: N.119, T.121, N.122, V.124 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: E.129, N.161 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: T.105, N.230 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: E.277, N.278 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.327, Q.576, T.577 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.339 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.599 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: N.612, T.614, W.629, Q.640, T.641 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: Y.651, V.652, N.653 Ligand excluded by PLIP NAG.11: 5 residues within 4Å: Chain A: Y.703, S.704, N.705 Chain B: I.790, Y.792 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.713, L.918, Q.1067 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.797, S.799, Q.800 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: A.702, N.1070 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: N.1094, G.1095, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.1130 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: Y.25, F.56, N.58 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: N.119, T.121, N.122, V.124 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: E.129, N.161 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: E.461 Chain B: T.105, N.230 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: K.554 Chain B: N.276, E.277, N.278 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.327, Q.576, T.577 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.339 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.599 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: N.612, T.614, Q.640, T.641 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: Y.651, V.652, N.653 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain B: Y.703, S.704, N.705 Chain C: I.790, Y.792 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.713, Q.1067 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.797, S.799, Q.800 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.1070 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain B: N.1094, G.1095, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.1130 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.119, T.121, N.122 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: Q.112, E.129, N.161, C.162 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: E.461 Chain C: T.105, N.230, T.232 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: E.277, N.278 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.327, Q.576, T.577 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: H.335, N.339 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.599 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.612, T.614, Q.640 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: Y.651, N.653 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain A: I.790, Y.792 Chain C: Y.703, S.704, N.705 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.713, L.918, Q.1067 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.797, S.799, Q.800 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: A.702, N.1070 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: N.1094, T.1096, F.1099 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.1130 Ligand excluded by PLIP

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

IDU.33: 5 residues within 4Å: Chain A: R.351, R.462 Chain B: Q.112, I.227, G.228 No protein-ligand interaction detected (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
B

B
A

C
C

Spike glycoprotein