SMTL ID : 7z8o.1

Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.96 Å

Oligo State

hetero-1-1-mer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: W.107, N.108, S.109, N.111, L.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.107, A:S.109, A:N.111, A:L.112 GOL.2: 3 residues within 4Å: Chain B: X.1, C.2, P.3 No protein-ligand interaction detected (PLIP) GOL.3: 4 residues within 4Å: Chain A: T.141, F.161 Chain B: Y.4, T.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.4

1 x KZ0: 2,4,6-tris(chloromethyl)-1,3,5-triazine(Covalent)

KZ0.4: 6 residues within 4Å: Chain A: Y.120 Chain B: C.2, P.3, T.10, C.11, C.14 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.3, A:Y.120, A:Y.120 pi-Stacking: A:Y.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gaynor, K.U. et al., Multivalent bicyclic peptides are an effective antiviral modality that can potently inhibit SARS-CoV-2. Nat Commun (2023)

Release Date

2023-06-28

Peptides

Spike protein S1: A
Stapled peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Spike protein S1

Stapled peptide

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