SMTL ID : 7yi6.2 (1 other biounit)

bnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-1-1-mer

Ligands

1 x VAL- VAL- ASN- GLN- GLN- GLY: Spike glycoprotein(Non-covalent)

VAL-VAL-ASN-GLN-GLN-GLY.1: 16 residues within 4Å: Chain A: Y.30, Y.32, Y.91 Chain B: T.30, S.31, L.32, S.33, N.35, W.50, S.52, T.53, K.54, P.102, V.103, G.104, W.105 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.50, B:W.50, B:V.103, B:W.105, A:Y.30, A:Y.32, A:Y.91 Hydrogen bonds: B:S.33, B:N.35, B:N.35, B:S.52, B:T.53, B:T.53, B:K.54, B:V.103, A:Y.91 Water bridges: B:P.102, B:V.103

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 4 residues within 4Å: Chain A: A.159, G.160, E.162, S.181 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.160, A:E.162, A:S.181 Water bridges: A:V.161

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: Q.169, S.170 Chain B: H.171 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:V.170, A:N.171 Hydrogen bonds: A:S.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, L. et al., Cross-reactive epitopes between HIV and Coronavirus revealed by 3D1. To Be Published

Release Date

2023-08-30

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

light chain of 3D1

heavy chain of 3D1

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