SMTL ID : 8wgw.1

Local refinement of RBD-ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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: 5 residues within 4Å: Chain B: H.417, S.420, D.543, S.545, N.546 No protein-ligand interaction detected (PLIP)

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

NAG.2: 1 residues within 4Å: Chain A: N.340 No protein-ligand interaction detected (PLIP) NAG.3: 1 residues within 4Å: Chain B: N.322 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain B: N.432 No protein-ligand interaction detected (PLIP) NAG.5: 4 residues within 4Å: Chain B: Q.81, Q.101, N.103, H.195 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain B: K.26, N.90 No protein-ligand interaction detected (PLIP) NAG.7: 5 residues within 4Å: Chain B: N.53, T.55, E.57, V.339, Q.340 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.57

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 2 residues within 4Å: Chain B: H.374, E.402 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.402

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, X. et al., The receptor binding domain of SARS-CoV-2 Omicron subvariants targets Siglec-9 to decrease its immunogenicity by preventing macrophage phagocytosis. Nat.Immunol. (2024)

Release Date

2024-02-28

Peptides

Spike glycoprotein: A
Angiotensin-converting enzyme 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Spike glycoprotein

Angiotensin-converting enzyme 2

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