SMTL ID : 8iot.1

Structure of the SARS-CoV-2 XBB.1 spike glycoprotein (closed-2 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.3: 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.4: 3 residues within 4Å: Chain B: N.796, S.798, Q.799 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 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.6: 3 residues within 4Å: Chain C: N.796, S.798, Q.799 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain A: Y.24, T.25, N.57 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.118, T.120, N.121, V.123 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.159, N.160 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: T.104, N.229 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.277 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.611, Q.639 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.652 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.704 Chain C: Y.791 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: A.701, E.1067, N.1069 Chain C: Q.890 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.1093, T.1095, H.1096, F.1098 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.1129 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: H.334, N.338, F.366 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: Y.24, T.25, N.57 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.118, T.120, N.121, V.123 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.159, N.160 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: T.104, N.229 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.277 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.611, Q.639 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.652 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: Y.791 Chain B: N.704 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: Q.890 Chain B: A.701, E.1067, N.1069 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.1093, T.1095, H.1096, F.1098 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1129 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: H.334, N.338, F.366 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: Y.24, T.25, N.57 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: N.118, T.120, N.121, V.123 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.159, N.160 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: T.104, N.229 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.277 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.611, Q.639 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.652 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: Y.791 Chain C: N.704 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: Q.890 Chain C: A.701, E.1067, N.1069 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.1093, T.1095, H.1096, F.1098 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.1129 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: H.334, N.338, F.366 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tamura, T. et al., Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants. Nat Commun (2023)

Release Date

2023-05-24

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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