SMTL ID : 9eli.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.82 Å

Oligo State

homo-trimer

Ligands

6 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.1: 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.5: 3 residues within 4Å: Chain A: N.792, S.794, Q.795 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 4 residues within 4Å: Chain B: N.708, L.913, Q.917, Q.1062 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.913 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.11: 4 residues within 4Å: Chain C: N.708, L.913, Q.917, Q.1062 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.913 NAG-NAG-BMA.15: 3 residues within 4Å: Chain C: N.792, S.794, Q.795 No protein-ligand interaction detected (PLIP)

9 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 4 residues within 4Å: Chain A: N.1089, T.1091, H.1092, F.1094 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1125 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: E.273, N.274 Chain B: K.549 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1089, T.1091, H.1092, F.1094 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1125 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: E.273, N.274 Chain C: K.549 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.1089, T.1091, H.1092, F.1094 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain C: N.1125 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain A: K.549 Chain C: E.273, N.274 No protein-ligand interaction detected (PLIP)

21 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 C: L.840 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.700 Chain C: I.785, Y.787 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: A.697, N.1065 Chain C: Q.886 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: R.338, F.339, A.340, N.346 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.335 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: T.102, N.226, T.228 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: Y.25, N.27 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: L.840 Chain B: N.607, Q.635 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: I.785, Y.787 Chain B: N.700 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: Q.886 Chain B: A.697, N.1065 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: R.338, F.339, A.340, N.346 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.335 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: T.102, N.226, T.228 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: Y.25, N.27 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: L.840 Chain C: N.607, Q.635 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: I.785, Y.787 Chain C: N.700 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: Q.886 Chain C: A.697, N.1065 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: R.338, F.339, A.340, N.346 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.335 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: T.102, N.226, T.228 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: Y.25, N.27 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

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