SMTL ID : 7y8j.1

3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.03 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ASP- VAL- VAL- ASN- GLN- ASN- GLY: Spike protein S2'(Non-covalent)

ASP-VAL-VAL-ASN-GLN-ASN-GLY.1: 20 residues within 4Å: Chain A: T.30, S.31, L.32, S.33, N.35, W.47, W.50, S.52, T.53, K.54, G.99, P.102, V.103, G.104, W.105, F.107 Chain B: Y.34, Y.36, Y.95, S.99 26 PLIP interactions: 6 interactions with chain B, 20 interactions with chain A Hydrophobic interactions: B:Y.34, B:Y.95, B:S.99, A:S.33, A:W.50, A:V.103, A:W.105, A:W.105 Hydrogen bonds: B:Y.34, B:Y.95, B:Y.95, A:S.31, A:L.32, A:S.33, A:S.33, A:N.35, A:W.50, A:S.52, A:T.53, A:K.54, A:P.102, A:V.103, A:G.104, A:W.105 Water bridges: A:S.52, A:V.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, L. et al., A broadly neutralizing antibody recognizes a unique epitope with a signature motif common across coronaviruses. Nat Commun (2025)

Release Date

2023-07-12

Peptides

heavy chain of 3D1: A
light chain of 3D1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

heavy chain of 3D1

light chain of 3D1