SMTL ID : 7yow.2 (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

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

SO4.1: 3 residues within 4Å: Chain A: Q.37, K.39, 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 SO4.2: 2 residues within 4Å: Chain A: S.7, S.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.7, A:S.9 SO4.3: 6 residues within 4Å: Chain B: E.152, P.153, V.154, F.170, A.172, L.182 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.154, B:A.172 SO4.4: 7 residues within 4Å: Chain A: I.29, H.32, H.90, N.92, S.93 Chain C: R.83, H.185 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Salt bridges: C:R.83, C:H.185, A:H.32, A:H.90 Hydrogen bonds: A:S.93 SO4.5: 7 residues within 4Å: Chain A: S.30, S.31, H.32 Chain C: Y.129, S.176, R.178, Y.181 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:Y.129, C:S.176, C:R.178, C:Y.181, A:S.30, A:S.30, A:S.31 Salt bridges: A:H.32

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
A

B
B

C
C

Fab Light chain

Fab Heavy chain

Spike protein S1

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