SMTL ID : 8xn5.1

Cryo-EM structure of SARS-CoV-2 Omicron EG.5.1 spike protein(6P) in complex with human ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.35, T.37, E.39, N.40, Q.322 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: Q.63, Q.83, N.85 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: D.413, N.414, E.415 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.528 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.304 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain B: N.43 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain B: N.104, A.105, T.106 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain B: N.215 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain B: N.261, E.262, N.263 Chain C: K.539 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain B: N.597, Q.625 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain B: N.1079, T.1081, H.1082, F.1084 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain B: N.1115 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: P.311, N.312, P.560, Q.561 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: N.698, L.903, Q.907, Q.1052 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.782, S.784 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: N.690 Chain D: I.775, Y.777 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain C: N.312, Q.561 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain C: Y.10, N.43 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: N.104, T.106, V.109 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: T.90, N.215 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: E.262, N.263 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain C: N.597 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: Y.777 Chain C: N.690, N.691 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: N.1079, T.1081, H.1082, F.1084 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.1115 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.782, S.784, Q.785 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain C: T.697, N.698, L.903, Q.907, Q.1052 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: N.698, Q.1052 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain D: N.782, S.784, Q.785, N.909 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain D: N.104, T.106, N.107, V.109 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: E.114, N.146 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain D: E.262, N.263, T.265 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: I.775, Y.777 Chain D: N.690 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain D: N.1079, T.1081, H.1082, F.1084 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain D: N.1115 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain D: N.597, T.599 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 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

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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