SMTL ID : 7zf3.1

SARS-CoV-2 Omicron RBD in complex with Omi-3 and EY6A Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

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

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain B: Q.37, R.61, E.81, D.82 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.37, B:R.61, B:D.82, B:D.82 GOL.2: 1 residues within 4Å: Chain B: Y.32 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.32, B:Y.32 GOL.5: 4 residues within 4Å: Chain C: W.47 Chain D: S.94, P.96, T.99 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.94, D:T.99 GOL.6: 2 residues within 4Å: Chain E: G.78, Y.182 No protein-ligand interaction detected (PLIP)

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.3: 3 residues within 4Å: Chain C: G.8, R.19, S.21 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.19 IPA.4: 4 residues within 4Å: Chain C: S.7, G.8, G.9, K.206 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.206 Hydrogen bonds: C:G.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nutalai, R. et al., Potent cross-reactive antibodies following Omicron breakthrough in vaccinees. Cell (2022)

Release Date

2022-06-01

Peptides

EY6A heavy chain: A
EY6A light chain: B
Omi-3 heavy chain: C
Omi-3 light chain: D
Spike protein S1: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

D
B

E
E

EY6A heavy chain

EY6A light chain

Omi-3 heavy chain

Omi-3 light chain

Spike protein S1

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