SMTL ID : 9atm.1

SARS-CoV-2 EG.5 RBD bound to the VIR-7229 and the S2H97 Fab fragments

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

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

Ligands

3 x EDO: 1,2-ETHANEDIOL(Non-covalent)(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain B: Y.52, D.55 Chain E: K.116, K.152, L.153, K.154 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain B Water bridges: E:K.116, E:K.116, E:K.152, E:K.152 Hydrogen bonds: B:D.55 EDO.5: 4 residues within 4Å: Chain E: W.45, N.46, R.47, R.158 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.46, E:R.47 EDO.7: 4 residues within 4Å: Chain E: A.68, G.96, V.99, Y.200 No protein-ligand interaction detected (PLIP)

1 x NI: NICKEL (II) ION(Non-functional Binders)

NI.2: 1 residues within 4Å: Chain C: D.142 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 1 residues within 4Å: Chain C: H.192 Ligand excluded by PLIP

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Post Translational Modification)

TRS.4: 6 residues within 4Å: Chain B: G.169, H.171, T.190 Chain D: S.143, D.144, Q.173 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:G.169, B:T.190, D:S.143, D:D.144

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG.6: 3 residues within 4Å: Chain E: N.35, N.62, F.63 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.63 Hydrogen bonds: E:N.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rosen, L.E. et al., A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification. Cell (2024)

Release Date

2024-10-16

Peptides

VIR-7229 Fab heavy chain: A
S2H97 Fab heavy chain: B
VIR-7229 Fab light chain: C
S2H97 Fab light chain: D
SARS-CoV-2 EG.5 RBD: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
L

D
M

E
R

VIR-7229 Fab heavy chain

S2H97 Fab heavy chain

VIR-7229 Fab light chain

S2H97 Fab light chain

SARS-CoV-2 EG.5 RBD

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