SMTL ID : 8cbf.1

SARS-CoV-2 Delta-RBD complexed with Omi-42 and Beta-49 Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

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

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- FUC: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-MAN-MAN-FUC.1: 14 residues within 4Å: Chain A: F.16, N.17, A.18, S.45, A.46, S.47, L.115 Chain B: Y.50, T.57 Chain C: S.100, A.103, I.105, F.107 Ligands: GOL.4 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:S.47, A:S.47 Hydrophobic interactions: C:I.105, C:F.107 Water bridges: B:T.57

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: S.49, T.50, V.81, Y.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.50, A:T.50, A:Y.182 GOL.3: 3 residues within 4Å: Chain A: Y.43, S.45, F.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.43 GOL.4: 6 residues within 4Å: Chain A: F.16, N.17, S.47, F.48, W.110 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-FUC.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.16, A:N.17, A:S.47, A:S.47

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: Y.123 Chain B: R.55, S.64 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.55

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain B: T.99, F.100 Chain C: E.46, W.47 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection. Nat Commun (2024)

Release Date

2024-02-07

Peptides

Spike protein S1: A
Beta-49 light chain: B
Beta-49 heavy chain: C
Omi-42 light chain: D
Omi-42 heavy chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
B

C
A

D
L

E
H

Spike protein S1

Beta-49 light chain

Beta-49 heavy chain

Omi-42 light chain

Omi-42 heavy chain

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