SMTL ID : 8c3v.1 (2 other biounits)

SARS-CoV-2 Delta-RBD complexed with BA.2-13 Fab and C1 nanobody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-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-MAN-FUC.1: 5 residues within 4Å: Chain C: F.12, G.13, F.16, N.17 Ligands: PG0.4 No protein-ligand interaction detected (PLIP)

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: T.106, L.107, L.108 Chain C: F.21, S.23, N.124, Y.125, R.126 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.23, C:S.23, C:Y.125, C:R.126, A:L.108, A:L.108 GOL.3: 6 residues within 4Å: Chain C: V.36, A.37, L.61, N.62, L.64, F.66 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.37, C:N.62 GOL.5: 7 residues within 4Å: Chain C: F.48, S.49 Chain D: W.50, T.59, Y.60, R.104, T.106 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.49, D:Y.60, D:R.104 GOL.6: 5 residues within 4Å: Chain C: V.177, Y.182 Chain D: R.45, T.106, P.108 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:T.106, D:T.106, C:Y.182, C:Y.182 GOL.7: 6 residues within 4Å: Chain D: F.27, T.28, N.29, D.30, Y.32, N.77 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:F.27, D:T.28, D:Y.32, D:N.77

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.4: 6 residues within 4Å: Chain C: N.17, S.45, S.47, F.48, W.110 Ligands: NAG-NAG-BMA-MAN-FUC.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.45, C:S.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dijokaite-Guraliuc, A. et al., Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses. Cell Rep (2023)

Release Date

2023-03-22

Peptides

BA.2-13 heavy chain: A
BA.2-13 light chain: B
Spike protein S1: C
Nanobody C1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
R

D
I

BA.2-13 heavy chain

BA.2-13 light chain

Spike protein S1

Nanobody C1

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