SMTL ID : 9ml8.4 (3 other biounits)

Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-B1 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: F.11, G.12, F.15, N.16, V.40, L.41, S.44 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.44

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

SO4.2: 4 residues within 4Å: Chain A: E.79, Q.82, G.89, K.90 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.82, A:K.90, A:I.91 Water bridges: A:R.76, A:D.78 SO4.3: 3 residues within 4Å: Chain C: P.60, R.62, D.82 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, C. et al., Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-06-04

Peptides

Spike protein S1: A
M8b-B1 heavy chain: B
M8b-B1 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
P

C
Q

Spike protein S1

M8b-B1 heavy chain

M8b-B1 light chain

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