SMTL ID : 8c3v.3 (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-(1-6)-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 A: F.12, G.13, F.16, N.17 Ligands: PG4.4 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: C.35, V.36, A.37, Y.39, L.61, N.62, L.64, F.66 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.35, A:A.37, A:L.64, A:L.64 GOL.3: 8 residues within 4Å: Chain A: F.21, S.23, N.124, Y.125, R.126 Chain C: T.106, L.107, L.108 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.23, A:S.23, A:Y.125, A:R.126, C:L.108 GOL.5: 4 residues within 4Å: Chain B: N.29, D.30, F.31, S.54 No protein-ligand interaction detected (PLIP) GOL.6: 4 residues within 4Å: Chain A: Y.182 Chain B: T.106, W.107, P.108 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.182, B:T.106, B:T.106

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 7 residues within 4Å: Chain A: N.17, L.42, S.45, S.47, F.48, W.110 Ligands: NAG-NAG-BMA-MAN-FUC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.45

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Y

B
K

C
C

D
D

Spike protein S1

Nanobody C1

BA.2-13 heavy chain

BA.2-13 light chain

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