SMTL ID : 7xxk.3 (2 other biounits)

Crystal structure of SARS-CoV-2 N-CTD in complex with GMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: K.12, R.18, T.19 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: K.22, R.49, Q.50 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain B: R.18, T.19 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: A.67 Chain B: W.57 Ligand excluded by PLIP

1 x GMP: GUANOSINE(Non-covalent)

GMP.3: 6 residues within 4Å: Chain A: R.15, T.38, W.86 Chain B: M.73, I.93, K.94 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:A.92, B:K.94, B:K.94, A:R.15, A:T.38 pi-Stacking: A:W.86 pi-Cation interactions: A:R.15, A:R.15

1 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: T.19 Chain B: S.66, A.67, S.68 No protein-ligand interaction detected (PLIP)

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

NA.7: 3 residues within 4Å: Chain B: Q.59, D.104, Q.105 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.62, B:N.101, B:D.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ni, X. et al., Structural basis of the C-terminal domain of SARS-CoV-2 N protein in complex with GMP reveals critical residues for RNA interaction. Bioorg.Med.Chem.Lett. (2024)

Release Date

2022-06-29

Peptides

Nucleoprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Nucleoprotein

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