SMTL ID : 8sdf.2 (1 other biounit)

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC25.4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: F.6, G.7, F.10, N.11, V.35, L.36 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.10, A:L.36 Hydrogen bonds: A:N.11

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 1 residues within 4Å: Chain A: L.120 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.120 MPD.3: 4 residues within 4Å: Chain B: N.212, K.214, N.217, K.219 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.214, B:K.219 Hydrogen bonds: B:N.212, B:N.217, B:K.219 MPD.4: 8 residues within 4Å: Chain B: G.42, Q.43 Chain C: P.8, D.86, Y.88, G.104, G.105, K.107 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.8, C:D.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, G. et al., Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift. Biorxiv (2023)

Release Date

2024-03-13

Peptides

Spike protein S1: A
Neutralizing antibody CC25.4 heavy chain: B
Neutralizing antibody CC25.4 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike protein S1

Neutralizing antibody CC25.4 heavy chain

Neutralizing antibody CC25.4 light chain

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