SMTL ID : 8xux.1

Structure of the SARS-CoV-2 BA.2.86 spike protein (1-up state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

7 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: 2 residues within 4Å: Chain A: N.702, L.907 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.786, S.788, Q.789 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: N.702, Q.911, Q.1056 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.786, S.788, Q.789 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain C: K.101, Q.103, V.118, E.120, N.152, T.154 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.101 NAG-NAG.6: 3 residues within 4Å: Chain C: N.702, L.907, Q.1056 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: N.786, S.788 No protein-ligand interaction detected (PLIP)

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

NAG.8: 2 residues within 4Å: Chain A: Y.18, N.51 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.110, T.112, N.113, F.115 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.151, N.152 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: T.96, N.220, T.222 Chain B: E.451 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.268, T.270 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.601, T.603 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.642 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.694 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: A.691, E.1057, K.1058, N.1059 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.1083, H.1086, F.1088 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.1119 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.317, Q.565 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.329 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: R.332, F.333, A.334, N.340 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.110, N.113, E.143 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.152 Ligands: NAG.42 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.220 Chain C: E.451 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: E.267, N.268 Chain C: K.543 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.601, T.603 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.640, N.642 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: Y.781 Chain B: N.694 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: A.691, E.1057, N.1059 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.1083, T.1085, H.1086 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.1119 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: V.327, T.331, F.333, N.340 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: Y.18, N.51 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: N.110, T.112, N.113, F.115 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain A: K.543 Chain C: N.266, E.267, N.268 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.601, T.603, E.604 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: Y.640, N.642 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: I.779 Chain C: N.694 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: E.1057, K.1058, N.1059 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.1083, T.1085, H.1086, F.1088 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.1119 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.340 Ligands: NAG.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tamura, T. 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
B

C
C

Spike glycoprotein

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