SMTL ID : 9c6y.2 (1 other biounit)

Crystal structure of SARS-CoV-2 XBB.1.5 RBD bound to COV2-3906 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

hetero-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: 3 residues within 4Å: Chain C: F.11, N.13, N.42 No protein-ligand interaction detected (PLIP)

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

CL.2: 2 residues within 4Å: Chain B: K.160, A.161 Ligand excluded by PLIP

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

NAG.3: 2 residues within 4Å: Chain C: H.21, N.25 No protein-ligand interaction detected (PLIP)

1 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Post Translational Modification)

A2G.4: 5 residues within 4Å: Chain C: T.5, S.7, H.201, A.202, P.203 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.7

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

SO4.5: 4 residues within 4Å: Chain C: G.184, V.185, G.186, H.187 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.184, C:G.186, C:H.187 Salt bridges: C:H.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zost, S.J. et al., Epitope-focused discovery of SARS-CoV-2 antibodies that potently neutralize Omicron variants. To Be Published

Release Date

2025-10-08

Peptides

Heavy chain of COV2-3906 Fab: A
Light chain of COV2-3906 Fab: B
Spike protein S2': C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
F

Heavy chain of COV2-3906 Fab

Light chain of COV2-3906 Fab

Spike protein S2'

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