SMTL ID : 7wnb.1

Crystal structure of SARS-CoV-2 spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: G.19, F.22, N.23, V.47 No protein-ligand interaction detected (PLIP)

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

SO4.2: 4 residues within 4Å: Chain B: Q.37, K.39, K.42, K.45 5 PLIP interactions: 5 interactions with chain B Water bridges: B:Q.37, B:K.39 Salt bridges: B:K.39, B:K.42, B:K.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shitaoka, K. et al., Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants. Commun Biol (2023)

Release Date

2023-04-19

Peptides

Spike protein S1: A
Fab Light chain: B
Fab Heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
L

C
H

Spike protein S1

Fab Light chain

Fab Heavy chain

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