SMTL ID : 7yi6.1 (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 ASP- VAL- VAL- ASN- GLN- GLN- GLY: Spike glycoprotein(Non-covalent)

ASP-VAL-VAL-ASN-GLN-GLN-GLY.1: 16 residues within 4Å: Chain A: Y.30, Y.91, S.95 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 13 PLIP interactions: 2 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:Y.30, B:W.50, B:W.105 Hydrogen bonds: A:Y.91, B:S.33, B:N.35, B:N.35, B:S.52, B:T.53, B:T.53, B:K.54, B:V.103 Water bridges: B:W.50

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

EDO.2: 6 residues within 4Å: Chain A: E.83, V.107, Q.110, Y.142, N.172, Y.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.107, A:N.172, A:Y.174 EDO.3: 3 residues within 4Å: Chain A: R.61, S.76, G.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.76 EDO.5: 5 residues within 4Å: Chain B: E.10, K.12, S.17, V.18, R.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.10, B:K.12, B:R.19 EDO.6: 2 residues within 4Å: Chain B: S.119, S.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.120, B:S.120

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: P.59, R.61, E.81 Ligand excluded by PLIP

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
B

B
D

light chain of 3D1

heavy chain of 3D1

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