SMTL ID : 8jym.3 (2 other biounits)

Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

2 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.712, L.917 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.917 NAG-NAG.2: 2 residues within 4Å: Chain A: N.796, S.798 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: Y.24, N.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.24 NAG.4: 3 residues within 4Å: Chain A: N.118, T.120, V.123 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.120 Hydrogen bonds: A:T.120, A:T.120 NAG.5: 1 residues within 4Å: Chain A: N.160 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain A: T.104, N.229, T.231 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.104 NAG.7: 3 residues within 4Å: Chain A: N.275, E.276, N.277 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.275, A:E.276, A:E.276 NAG.8: 2 residues within 4Å: Chain A: N.611, Q.639 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.611 NAG.9: 2 residues within 4Å: Chain A: Y.650, N.652 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain A: N.704 No protein-ligand interaction detected (PLIP) NAG.11: 4 residues within 4Å: Chain A: A.701, E.1067, K.1068, N.1069 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.1067 NAG.12: 4 residues within 4Å: Chain A: N.1093, T.1095, H.1096, F.1098 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.1093, A:T.1095 NAG.13: 1 residues within 4Å: Chain A: N.1129 No protein-ligand interaction detected (PLIP) NAG.14: 4 residues within 4Å: Chain A: H.334, N.338, T.340, F.366 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tamura, T. et al., Virological characteristics of the SARS-CoV-2 XBB.1.5 variant. To Be Published

Release Date

2024-01-03

Peptides

Spike glycoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Spike glycoprotein

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