SMTL ID : 8gb8.1

Crystal structure of SARS-CoV-2 BA.2 receptor binding domain in complex with neutralizing antibody 20A7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.25, A.26, T.27 No protein-ligand interaction detected (PLIP)

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

EDO.2: 5 residues within 4Å: Chain A: R.85, Y.177, F.179, Y.183, H.187 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.85, A:H.187, A:H.187 EDO.6: 6 residues within 4Å: Chain C: V.29, G.31, S.32, L.33, G.50, A.51 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.33 EDO.7: 3 residues within 4Å: Chain C: S.52, S.53, R.54 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.54

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain B: F.174, P.175, V.177, S.185, L.186, S.187 Chain C: Q.160, S.162, S.176, S.177, T.178 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.162, C:S.176, C:T.178, B:P.175, B:S.185, B:S.187

1 x GLY: GLYCINE(Non-covalent)

GLY.4: 2 residues within 4Å: Chain C: N.210, R.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.211

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

PEG.5: 7 residues within 4Å: Chain B: G.42, K.43 Chain C: A.9, V.85, Y.87, P.100, G.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.42 Water bridges: B:Q.39, B:K.43

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
20A7 Heavy chain: B
20A7 Light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
H

C
L

Spike protein S1

20A7 Heavy chain

20A7 Light chain

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