SMTL ID : 9elh.1

Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein (one RBD up state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.98 Å

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: 1 residues within 4Å: Chain A: N.1126 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: S.700, N.701 Chain C: Y.788 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.788 NAG-NAG.6: 4 residues within 4Å: Chain B: N.1090, T.1092, H.1093, F.1095 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.1126 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.273, E.274, N.275 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 7 residues within 4Å: Chain A: R.450, K.451, K.455, E.458 Chain B: T.102, N.227, T.229 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1126 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.793, S.795, Q.796 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain A: N.709, L.914, Q.918, Q.1063 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.914 NAG-NAG-BMA.4: 4 residues within 4Å: Chain A: N.1090, T.1092, H.1093, F.1095 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 3 residues within 4Å: Chain B: N.793, S.795, Q.796 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 4 residues within 4Å: Chain C: N.1090, T.1092, H.1093, F.1095 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 3 residues within 4Å: Chain C: N.793, S.795, Q.796 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 4 residues within 4Å: Chain C: N.709, L.914, Q.918, Q.1063 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.914

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

NAG.15: 4 residues within 4Å: Chain A: N.608, T.610, Q.636 Chain B: Y.829 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.701 Chain B: Y.788 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.1066 Ligand excluded by PLIP NAG.18: 6 residues within 4Å: Chain A: T.102, N.227, T.229 Chain C: E.458, R.459, D.460 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: E.274, N.275 Chain C: K.550 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.324, P.571, Q.572 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: R.339, N.347, T.349 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: Y.647, V.648, N.649 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: H.332, N.336 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: Y.25, T.26, N.27, D.208, P.210 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: N.608, Q.636 Chain C: Q.828, Y.829 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.709, Q.1063 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: A.698, N.1066 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.27 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: H.332, N.336, F.364 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain A: Y.344, I.461 Chain B: A.156, N.157, N.158 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: Q.828 Chain C: N.608, T.610 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: I.786, Y.788 Chain C: N.701 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: A.698, N.1066 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.324, L.574 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.273, N.275 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.347, T.349 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: H.332, N.336 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: Y.25, N.27, Q.211 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, Z., Structure of SARS-CoV-2 KP.3.1.1 Spike Protein. To Be Published

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