SMTL ID : 8we4.1

SARS-CoV-2 Omicron XBB.1.5 RBD complexed with human ACE2 and S304

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 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: 2 residues within 4Å: Chain A: Q.81, N.103 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 3 residues within 4Å: Chain A: S.420, D.543, N.546 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: N.53, Q.340 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.53, A:Q.340 NAG.4: 1 residues within 4Å: Chain A: N.90 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.90 NAG.5: 1 residues within 4Å: Chain A: N.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.322 NAG.6: 2 residues within 4Å: Chain A: N.432, E.433 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain B: N.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.25

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: H.374, E.375, H.378, E.402 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.374, A:H.378, A:E.402

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins. Embo J. (2024)

Release Date

2024-07-24

Peptides

Angiotensin-converting enzyme 2: A
Spike protein S1: B
S304 Fab Heavy Chain: C
S304 Fab Light Chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

Angiotensin-converting enzyme 2

Spike protein S1

S304 Fab Heavy Chain

S304 Fab Light Chain

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