SMTL ID : 9cpr.1

Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-90 and CC12.3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: F.6, G.7, F.10, N.11, V.35 No protein-ligand interaction detected (PLIP)

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 10 residues within 4Å: Chain A: R.71, K.85, Y.121 Chain B: D.101, F.102 Chain C: Y.91, G.92, S.93, S.94, R.96 9 PLIP interactions: 3 interactions with chain C, 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:Y.91, C:Y.91, C:S.94, A:R.71, A:R.71, B:D.101 Salt bridges: A:R.71, A:K.85, A:K.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nair, U. et al., In vivo antibody diversification targeting a conserved coronavirus epitope. J.Exp.Med. (2025)

Release Date

2025-06-25

Peptides

Spike protein S1: A
CC12.3 Fab heavy chain: B
CC12.3 Fab light chain: C
M22-90 Fab heavy chain: D
M22-90 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

C
G

D
H

E
L

Spike protein S1

CC12.3 Fab heavy chain

CC12.3 Fab light chain

M22-90 Fab heavy chain

M22-90 Fab light chain

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