› 5x4s

X-ray diffraction
2.2Å resolution

Structure of the N-terminal domain (NTD)of SARS-CoV spike protein

Released:
DOI: 10.2210/pdb5x4s/pdb
PDB entry 5x4s coloured by chain, front view.
PDB entry 5x4s coloured by chain, side view.
PDB entry 5x4s coloured by chain, top view.
Source organism: Severe acute respiratory syndrome-related coronavirus
Primary publication:
Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains.
Yuan Y, Cao D, Zhang Y, Ma J, Qi J, Wang Q, Lu G, Wu Y, Yan J, Shi Y, Zhang X, Gao GF
Nat Commun 8 15092 (2017)
PMID: 28393837

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157797 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Spike protein S1 Chain: A
Molecule details ›
Chain: A
Length: 285 amino acids
Theoretical weight: 32.4 KDa
Source organism: Severe acute respiratory syndrome-related coronavirus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P59594 (Residues: 14-292; Coverage: 23%)
Gene names: 2, S
Sequence domains: Betacoronavirus-like spike glycoprotein S1, N-terminal

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
1 bound ligand:
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P6122
Unit cell:
a: 73.291Å b: 73.291Å c: 240.263Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.254 0.252 0.282
Expression system: Trichoplusia ni

Quick links

Citations

149 review citations

Origin and evolution of pathogenic coronaviruses.
Cui et al. (2019)
148 more

12 mentions without citation

Emerging strategies on in silico drug development against COVID-19: challenges and opportunities.
Yadav et al. (2020)
11 more