SMTL ID : 9elp.1

Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11.1+S31 deletion spike protein (one RBD up state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.94 Å

Oligo State

homo-trimer

Ligands

8 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: 1 residues within 4Å: Chain A: N.1125 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.700 Chain C: I.785, Y.787 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.787 NAG-NAG.6: 4 residues within 4Å: Chain B: N.1089, T.1091, H.1092, F.1094 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.1125 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: K.549 Chain B: N.272, N.274 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: N.323, Q.571 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain A: R.449, S.451, E.457 Chain B: N.226, T.228 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain C: N.1125 No protein-ligand interaction detected (PLIP)

7 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 3 residues within 4Å: Chain A: N.792, S.794, Q.795 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: N.708, L.913, Q.917, Q.1062 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.913 NAG-NAG-BMA.4: 4 residues within 4Å: Chain A: N.1089, T.1091, H.1092, F.1094 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain B: N.792, S.794, Q.795 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 4 residues within 4Å: Chain C: N.1089, T.1091, H.1092, F.1094 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 3 residues within 4Å: Chain C: N.792, S.794, Q.795 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 4 residues within 4Å: Chain C: N.708, L.913, Q.917, Q.1062 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.913, C:Q.917

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

NAG.16: 3 residues within 4Å: Chain A: N.607, Q.635 Chain B: I.825 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: S.699, N.700 Chain B: Y.787 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.1065 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: T.102, N.226 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: E.273, N.274 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.323, P.570, Q.571 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: R.338, A.340, N.346 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: Y.646, V.647, N.648 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: H.331, N.335 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.607, T.609 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.708, Q.1062 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.1065 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: Y.25, N.27, Q.210 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.607, T.609 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: Y.787 Chain C: N.700 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.323 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.274 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, Z. et al., Structural and functional insights into the evolution of SARS-CoV-2 KP.3.1.1 spike protein. Cell Rep (2025)

Release Date

2025-05-28

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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