SMTL ID : 9ml9.1

Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-C9 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: G.12, F.15, N.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.16

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 6 residues within 4Å: Chain A: S.48, T.49, G.77, V.80, V.176, Y.181 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.49, A:T.49 TRS.3: 3 residues within 4Å: Chain A: D.101 Chain B: S.29, H.30 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.101, B:H.30, B:K.72, B:K.72

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-C9 heavy chain: B
M8b-C9 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike protein S1

M8b-C9 heavy chain

M8b-C9 light chain

Related Entries With Identical Sequence