SMTL ID : 8x0x.1 (1 other biounit)

Crystal structure of JE-5C in complex with SARS-CoV-2 RBD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.45 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.5, G.6, F.9, N.10, V.34 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.5, A:F.9, A:V.34 Hydrogen bonds: A:N.10

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

SO4.2: 4 residues within 4Å: Chain A: R.124, K.125, S.126, E.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.126, A:E.132 Salt bridges: A:R.124, A:K.125 SO4.3: 7 residues within 4Å: Chain A: E.73, Q.76, G.83, K.84 Chain B: Y.52, R.100 Chain C: L.94 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.52, B:Y.52, A:E.73, A:Q.76, A:K.84 Salt bridges: B:R.100, A:K.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., The presence of broadly neutralizing anti-SARS-CoV-2 RBD antibodies elicited by primary series and booster dose of COVID-19 vaccine. Plos Pathog. (2024)

Release Date

2024-06-05

Peptides

Spike protein S1: A
Heavy chain of JE-5C Fab: B
Light chain of JE-5C Fab: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
H

C
L

Spike protein S1

Heavy chain of JE-5C Fab

Light chain of JE-5C Fab

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