› 7c53

X-ray diffraction
2.28Å resolution

Crystal Structure of SARS-CoV-2 HR1 motif in complex with pan-CoVs inhibitor EK1

Released:
DOI: 10.2210/pdb7c53/pdb
PDB entry 7c53 coloured by chain, front view.
PDB entry 7c53 coloured by chain, side view.
PDB entry 7c53 coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Structural and functional basis for pan-CoV fusion inhibitors against SARS-CoV-2 and its variants with preclinical evaluation.
Xia S, Lan Q, Zhu Y, Wang C, Xu W, Li Y, Wang L, Jiao F, Zhou J, Hua C, Wang Q, Cai X, Wu Y, Gao J, Liu H, Sun G, Münch J, Kirchhoff F, Yuan Z, Xie Y, Sun F, Jiang S, Lu L
OpenAccess logo Signal Transduct Target Ther 6 288 (2021)
PMID: 34326308

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-144650 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Spike protein S2' Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 107 amino acids
Theoretical weight: 11.66 KDa
Source organism: synthetic construct
Expression system: Escherichia coli
UniProt:
  • Canonical: P0DTC2 (Residues: 910-975; Coverage: 5%)
Gene names: 2, S

Ligands and Environments

1 bound ligand:
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: C2221
Unit cell:
a: 133.815Å b: 138.141Å c: 71.461Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.195 0.242
Expression system: Escherichia coli

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Citations

10 review citations

Drug Combinations as a First Line of Defense against Coronaviruses and Other Emerging Viruses.
White et al. (2021)
9 more

6 mentions without citation

Small molecules in the treatment of COVID-19.
Lei et al. (2022)
5 more