› 8zfv

X-ray diffraction
2Å resolution

Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ceftriaxone

Released:
DOI: 10.2210/pdb8zfv/pdb
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PDB entry 8zfv coloured by chain, front view.
PDB entry 8zfv coloured by chain, side view.
PDB entry 8zfv coloured by chain, top view.
Source organism: Severe acute respiratory syndrome coronavirus 2
Primary publication:
Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid.
Dhaka P, Mahto JK, Singh A, Kumar P, Tomar S
J Struct Biol 217 108197 (2025)
PMID: 40113149

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145015 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nucleoprotein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 175 amino acids
Theoretical weight: 19.57 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTC9 (Residues: 247-419; Coverage: 41%)
Gene name: N
Sequence domains: Coronavirus nucleocapsid

Ligands and Environments

3 bound ligands:
Ligand SO4 1 x SO4
Ligand 9F2 3 x 9F2
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P1
Unit cell:
a: 43.539Å b: 46.643Å c: 69.021Å
α: 106.66° β: 90.11° γ: 93.46°
R-values:
R R work R free
0.15 0.147 0.205
Expression system: Escherichia coli BL21(DE3)

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