SMTL ID : 8xlv.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 spike protein(6P), 1-RBD-up 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.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain C: N.797, S.799 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain C: N.328, Q.576 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: H.336, N.340, F.368 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: A.341, N.351, T.353 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: N.612, T.614 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.705 Chain B: Y.792 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.713, L.918, Q.922, Q.1067 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: A.702, N.1070 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.1130 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: T.107, N.231, T.233 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: R.343, F.344, A.345, N.351, S.396 Ligand excluded by PLIP NAG.15: 7 residues within 4Å: Chain A: H.336, F.339, N.340, F.368, A.369, P.370, F.371 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.612, T.614, Q.640 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: N.705 Chain C: K.791, Y.792 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: T.712, N.713, Q.922, Q.1067 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.1070, T.1072 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.1094, H.1097, F.1099 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.1130 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: K.554 Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.23: 8 residues within 4Å: Chain B: E.337, R.343, F.344, A.345, A.349, W.350, N.351, S.396 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain B: F.339, N.340, L.365, F.368, A.369, W.433 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.612, T.614 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: Y.792 Chain C: N.705 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.713, Q.922, Q.1067 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.1070 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.1130 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., Spike structures, receptor binding, and immune escape of recently circulating SARS-CoV-2 Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants. Structure (2024)

Release Date

2024-07-03

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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