SMTL ID : 8gb6.1

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 21B6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 5 residues within 4Å: Chain A: F.6, G.7, F.10, N.11, L.36 No protein-ligand interaction detected (PLIP)

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: Q.77, G.84, K.85 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.77, A:K.85 Water bridges: A:D.73 SO4.3: 4 residues within 4Å: Chain A: G.144, S.145, T.146, N.155 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.145, A:T.146, A:N.155 Water bridges: A:G.144 SO4.4: 3 residues within 4Å: Chain B: D.218, K.219, K.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.220 Salt bridges: B:K.219 SO4.5: 2 residues within 4Å: Chain B: E.1, R.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.1 Salt bridges: B:R.3 SO4.6: 3 residues within 4Å: Chain B: D.75, S.77, R.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.75, B:S.77 Salt bridges: B:R.78 SO4.7: 2 residues within 4Å: Chain B: R.107 Chain C: S.30 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.30 Water bridges: C:N.31, B:R.107, B:R.107 Salt bridges: B:R.107 SO4.8: 4 residues within 4Å: Chain B: K.224 Chain C: S.121, D.122, E.123 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Water bridges: B:K.224 Salt bridges: B:K.224 Hydrogen bonds: C:D.122, C:D.122, C:E.123 SO4.9: 3 residues within 4Å: Chain C: K.39, K.42, K.45 4 PLIP interactions: 4 interactions with chain C Water bridges: C:Q.37, C:K.42 Salt bridges: C:K.39, C:K.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, Y. et al., Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine. Sci Transl Med (2023)

Release Date

2023-05-24

Peptides

Spike protein S1: A
21B6 Heavy chain: B
21B6 Light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike protein S1

21B6 Heavy chain

21B6 Light chain

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