SMTL ID : 7sbu.1

Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a highly potent antibody J08 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: F.6, G.7, F.10, N.11, V.35 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.10 Hydrogen bonds: A:N.11

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain B: L.153, F.178, P.179, V.181, S.189, L.190, S.191 Chain C: Q.156, S.158, S.172, T.174 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.172, C:T.174, B:P.179, B:S.189, B:S.191 GOL.3: 7 residues within 4Å: Chain C: Q.37, L.47, P.59, R.61, F.62, E.81, D.82 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.37, C:R.61, C:E.81, C:D.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Torres, J.L. et al., Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-05-11

Peptides

Spike protein S1: A
J08 Fab heavy chain: B
J08 Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike protein S1

J08 Fab heavy chain

J08 Fab light chain

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