SMTL ID : 8tfd.1

Crystal structure of a stem-loop DNA aptamer complexed with SARS-CoV-2 nucleocapsid protein RNA-binding domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: Q.26, P.118, Q.119, G.120, T.121 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.26 EDO.2: 5 residues within 4Å: Chain A: L.12, L.115, Q.116, L.117, Y.128 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.117, A:L.117 Water bridges: A:L.115 EDO.3: 3 residues within 4Å: Chain A: N.82, K.83, D.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.82, A:D.84 Water bridges: A:K.83 EDO.4: 5 residues within 4Å: Chain A: W.8, N.31, N.33, I.102, I.113 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.31, A:N.33 EDO.5: 2 residues within 4Å: Chain A: R.48 Chain B: T.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.48 EDO.6: 4 residues within 4Å: Chain A: R.51 Chain B: C.6, A.7, T.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esler, M.A. et al., A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain. Nucleic Acids Res. (2024)

Release Date

2024-11-13

Peptides

Nucleoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Nucleoprotein