SMTL ID : 8s6m.1

SARS-CoV-2 BQ.1.1 RBD bound to the S2V29 and the S2H97 Fab fragments

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

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

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: G.42, K.43 Chain D: D.87, Y.89, G.104 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.87, D:Y.89 Water bridges: D:Q.106 EDO.2: 6 residues within 4Å: Chain B: K.116, K.152, L.153, K.154 Chain C: Y.52, D.55 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Water bridges: B:K.116, B:K.116, B:K.152 Hydrogen bonds: C:D.55 EDO.3: 4 residues within 4Å: Chain B: W.45, N.46, R.47, R.158 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.46, B:R.47 Water bridges: B:R.158 EDO.4: 6 residues within 4Å: Chain B: T.38, F.39, A.40, S.41, N.142, Y.143 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.41 Water bridges: B:S.41, B:N.140, B:N.142 EDO.6: 4 residues within 4Å: Chain B: A.68, G.96, V.99, Y.200 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain B: S.151 Chain C: D.55, S.56, D.57 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Water bridges: A:S.56, B:K.152, C:T.58 Hydrogen bonds: C:D.55 EDO.8: 6 residues within 4Å: Chain C: Q.99, H.102, Y.105 Chain E: Y.32, Y.93 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.99, C:Q.99 EDO.10: 4 residues within 4Å: Chain D: A.154, S.157, H.192 Ligands: NI.9 No protein-ligand interaction detected (PLIP) EDO.11: 6 residues within 4Å: Chain C: W.33, I.50, R.59 Chain E: Y.93, S.95 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.93, E:S.95

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

NAG.5: 3 residues within 4Å: Chain B: N.35, N.62, F.63 No protein-ligand interaction detected (PLIP)

1 x NI: NICKEL (II) ION(Non-covalent)

NI.9: 2 residues within 4Å: Chain D: H.192 Ligands: EDO.10 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.192, H2O.22

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.12: 6 residues within 4Å: Chain C: G.169, H.171 Chain E: S.143, D.144, Q.173, N.175 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:S.143, E:D.144, E:N.175, C:G.169 Water bridges: E:Q.173, E:N.175

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

2024-10-23

Peptides

S2V29 Fab heavy chain: A
Spike protein S1: B
S2H97 Fab heavy chain: C
S2V29 Fab light chain: D
S2H97 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
R

C
I

D
L

E
M

S2V29 Fab heavy chain

Spike protein S1

S2H97 Fab heavy chain

S2V29 Fab light chain

S2H97 Fab light chain

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