SMTL ID : 7uxz.1 (2 other biounits)

Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain complexed with Chicoric acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

1 x GKP: (2R,3R)-2,3-bis{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}butanedioic acid(Non-covalent)

GKP.1: 8 residues within 4Å: Chain A: N.19, T.21, R.26, R.27, Q.39, I.42, F.113, P.114 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.21, A:Q.39, A:F.113, A:F.113 Hydrogen bonds: A:T.21, A:R.27 Salt bridges: A:R.26, A:R.26

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: E.73, T.75, W.80, T.82 Chain B: A.86 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: A.58, P.59 Chain B: K.11, P.59, A.61 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.11 Water bridges: B:P.59, B:P.59, B:A.61, B:A.61, A:P.59, A:A.61

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 2 residues within 4Å: Chain A: V.100, N.104 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.104, A:N.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mercaldi, G.F. et al., Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor. Sci Rep (2022)

Release Date

2022-06-22

Peptides

Nucleoprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Nucleoprotein

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