SMTL ID : 7yow.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: S.30, S.31, H.32 Chain C: Y.129, R.173, S.176, R.178 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:R.173, C:S.176, C:R.178, A:S.30, A:S.30, A:S.31, A:S.31 Salt bridges: A:H.32 SO4.2: 4 residues within 4Å: Chain A: Q.37, K.39, K.42, K.45 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.37 Salt bridges: A:K.39, A:K.42, A:K.45 SO4.3: 4 residues within 4Å: Chain A: S.7, P.8, S.9, S.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.7, A:S.9, A:S.10 SO4.4: 5 residues within 4Å: Chain B: E.152, V.154, F.170, A.172, L.182 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.152, B:A.172 SO4.5: 2 residues within 4Å: Chain B: R.19, K.75 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.19 Salt bridges: B:K.75 SO4.6: 2 residues within 4Å: Chain B: R.71, N.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.73 Salt bridges: B:R.71 SO4.7: 3 residues within 4Å: Chain C: K.124, V.125, S.126 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.125 Salt bridges: C:K.124

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
R

Fab Light chain

Fab Heavy chain

Spike protein S1

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