SMTL ID : 8wxl.1

Structure of the SARS-CoV-2 BA.2.86 spike glycoprotein (closed state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.712, L.917, Q.1066 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.917 NAG-NAG.2: 3 residues within 4Å: Chain A: N.796, S.798, Q.799 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: N.712, L.917, Q.1066 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.917 NAG-NAG.17: 3 residues within 4Å: Chain B: N.796, S.798, Q.799 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain C: N.712, L.917, Q.1066 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.917 NAG-NAG.32: 3 residues within 4Å: Chain C: N.796, S.798, Q.799 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain A: N.120, T.122, N.123, F.125 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.161, N.162 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.652 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.704 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: A.701, E.1067, N.1069 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.1093, T.1095, H.1096, F.1098 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.1129 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: H.335, N.339, F.367 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: A.344, N.350 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.276, E.277, N.278 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.611, T.613, E.614 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.327, Q.575, T.576 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: N.120, T.122, N.123, F.125 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.161, N.162 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.652 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.704 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: A.701, E.1067, N.1069 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.1093, T.1095, H.1096, F.1098 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.1129 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: H.335, N.339, F.367 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: A.344, N.350 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.276, E.277, N.278 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.611, T.613, E.614 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.327, Q.575, T.576 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: N.120, T.122, N.123, F.125 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.161, N.162 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.652 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.704 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: A.701, E.1067, N.1069 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: N.1093, T.1095, H.1096, F.1098 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.1129 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: H.335, N.339, F.367 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: A.344, N.350 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: N.276, E.277, N.278 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.611, T.613, E.614 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.327, Q.575, T.576 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yajima, H. et al., Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1. Nat Commun (2024)

Release Date

2024-10-09

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Spike glycoprotein