SMTL ID : 8dv1.1

SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: F.342, N.343, L.368 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.342, A:L.368 NAG.2: 3 residues within 4Å: Chain B: V.299, L.303, N.305 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.299 NAG.3: 5 residues within 4Å: Chain B: Q.64, N.86, S.88, S.89, V.90 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.86, B:V.90 Hydrogen bonds: B:Q.64 NAG.4: 4 residues within 4Å: Chain B: F.268, N.415, E.416, I.419 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.268, B:E.416, B:I.419 NAG.5: 4 residues within 4Å: Chain B: H.400, S.403, I.404, N.529 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.404 NAG.6: 2 residues within 4Å: Chain B: Q.72, N.73 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain B: N.36, E.40, Q.323 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.40, B:N.41, B:Q.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Remesh, S.G. et al., Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps. Structure (2023)

Release Date

2022-08-31

Peptides

Spike glycoprotein: A
Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chain fusion,Immunoglobulin gamma-1 heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Spike glycoprotein

Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chain fusion,Immunoglobulin gamma-1 heavy chain

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