SMTL ID : 8xnf.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 spike protein(6P) in complex with human ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-mer

Ligands

1 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: 2 residues within 4Å: Chain B: N.705 Chain D: Y.792 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.792 Hydrogen bonds: D:Y.792

5 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: 2 residues within 4Å: Chain B: N.797, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: N.1094, T.1096, H.1097, F.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain C: N.797, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain D: N.797, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain D: N.1094, T.1096, H.1097, F.1099 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 3 residues within 4Å: Chain A: H.356, H.360, E.384 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.356, A:H.360, A:E.384, A:E.384

33 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.8: 3 residues within 4Å: Chain A: N.31, N.35, N.40 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.72, V.75 Ligand excluded by PLIP NAG.10: 5 residues within 4Å: Chain A: E.294, V.298, L.302, P.303, N.304 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: F.267, N.414, E.415 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: H.399, S.402, D.525, S.527, N.528 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: Q.63, N.85, S.88, V.89 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: N.277, E.278, N.279 Chain C: K.554 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.328, V.329, Q.576 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.612, T.614, Q.640 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.713, Q.1067 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: C.1078, H.1079, N.1130 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain B: R.343, F.344, A.345, N.351, S.396 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: H.336, N.340, F.368, A.369 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: N.612, T.614, E.615 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: Y.792 Chain C: S.704, N.705 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.713, Q.1067 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.1130 Ligand excluded by PLIP NAG.27: 6 residues within 4Å: Chain C: R.343, F.344, A.345, N.351, T.353, S.396 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.340, F.368 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: F.60, N.62 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain D: N.162, N.163 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain D: N.328, Q.576 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: N.612, Q.640 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: Y.792 Chain D: N.705 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: N.713, L.918 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain D: I.1128, V.1129, N.1130 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: K.554 Chain D: N.277, E.278, N.279 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain D: N.1070, F.1071, T.1072 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain D: Y.651, V.652, N.653 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain D: R.343, F.344, A.345, N.351, S.396 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain D: H.336, N.340, F.368 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

Angiotensin-converting enzyme 2: A
Spike glycoprotein: BCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Angiotensin-converting enzyme 2

Spike glycoprotein

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