SMTL ID : 8qrf.1

SARS-CoV-2 delta RBD complexed with XBB-6 and beta-49 Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

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

Ligands

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 13 residues within 4Å: Chain A: F.16, N.17, A.18, S.45, S.47, L.115, R.183 Chain B: Y.50 Chain C: T.28, S.100, A.103, I.105, F.107 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:T.28, C:F.107 Hydrogen bonds: A:S.47, A:S.47, B:T.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stuart, D.I. et al., The emerging BA.2.86 Omicron sub-lineage balances antibody escape and ACE2 affinity. To Be Published

Release Date

2024-05-08

Peptides

Spike protein S1: A
Beta-49 light chain: B
Beta-49 heavy chain: C
XBB-6 heavy chain: D
XBB-6 light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
B

C
A

D
H

E
L

Spike protein S1

Beta-49 light chain

Beta-49 heavy chain

XBB-6 heavy chain

XBB-6 light chain

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