SMTL ID : 9au1.1

SARS-CoV-2 XBB.1.5 RBD bound to the VIR-7229 and the S309 Fab fragments

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

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

Ligands

1 x K: POTASSIUM ION(Non-covalent)

K.1: 1 residues within 4Å: Chain B: S.202 No protein-ligand interaction detected (PLIP)

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

EDO.2: 7 residues within 4Å: Chain C: K.152, D.153, Q.180, S.186 Chain D: E.164, Y.181, S.183 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.186, C:S.186 EDO.5: 3 residues within 4Å: Chain C: G.26, I.27 Chain E: N.169 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:I.27, E:N.169, E:N.169

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 3 residues within 4Å: Chain C: G.42, K.43 Chain D: R.8 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:K.43 Salt bridges: C:K.43, D:R.8

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 5 residues within 4Å: Chain D: D.54, R.56 Chain E: Y.193, G.194, H.197 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:G.194, D:R.56 Salt bridges: E:H.197, D:D.54, D:D.54

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

NAG.6: 5 residues within 4Å: Chain A: Y.100 Chain B: Y.50 Chain E: H.31, F.34, N.35 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.34 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

S309 Fab heavy chain: A
S309 Fab light chain: B
VIR-7229 Fab heavy chain: C
VIR-7229 Fab light chain: D
SARS-CoV-2 XBB.1.5 RBD: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
N

C
H

D
L

E
R

S309 Fab heavy chain

S309 Fab light chain

VIR-7229 Fab heavy chain

VIR-7229 Fab light chain

SARS-CoV-2 XBB.1.5 RBD

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