SMTL ID : 7u8e.1

Crystal structure of antibody Ab246 in complex with SARS-CoV-2 receptor binding domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

CL.1: 1 residues within 4Å: Chain A: N.76 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: T.31, Y.33, H.52, H.53, S.54, K.56 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.53, A:S.54, A:S.54, A:S.54, A:K.56 GOL.3: 6 residues within 4Å: Chain A: G.8, P.9, G.10, V.12, L.18, S.19 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.9, A:T.17, A:S.19, A:S.19 GOL.4: 4 residues within 4Å: Chain B: R.198 Chain C: R.16, K.114, N.120 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:K.114, C:N.120, B:R.198, B:R.198 GOL.5: 6 residues within 4Å: Chain B: E.91, K.111, T.113, Y.149, K.175, Y.181 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.91, B:T.113, B:Y.149 GOL.7: 4 residues within 4Å: Chain C: E.76, Q.79, G.86, K.87 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.76, C:E.76, C:Q.79, C:K.87 GOL.8: 4 residues within 4Å: Chain B: Q.193, S.196, H.197 Chain C: N.110 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.193, B:S.196, B:S.196, C:N.110

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

NAG.6: 7 residues within 4Å: Chain B: E.192, K.195 Chain C: F.8, G.9, F.12, N.13, V.37 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.8, C:F.12 Hydrogen bonds: C:N.13, B:K.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sankhala, R.S. et al., Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain. Structure (2024)

Release Date

2023-03-15

Peptides

Antibody Ab246 Fab heavy chain: A
Antibody Ab246 Fab light chain: B
Spike protein S1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

Antibody Ab246 Fab heavy chain

Antibody Ab246 Fab light chain

Spike protein S1

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