› 7nkt

X-ray diffraction
2.3Å resolution

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-276079 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Spike protein S1 Chain: AAA
Molecule details ›
Chain: AAA
Length: 229 amino acids
Theoretical weight: 25.95 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DTC2 (Residues: 319-541; Coverage: 18%)
Gene names: 2, S
Sequence domains: Betacoronavirus spike glycoprotein S1, receptor binding
neutralizing nanobody NM1226 Chain: BBB
Molecule details ›
Chain: BBB
Length: 144 amino acids
Theoretical weight: 15.96 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli

Ligands and Environments

3 bound ligands:
Ligand NAG 1 x NAG
Ligand PO4 1 x PO4
Ligand PEG 3 x PEG
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X06DA
Spacegroup: I41
Unit cell:
a: 128.093Å b: 128.093Å c: 77.676Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.184 0.224
Expression systems:
  • Homo sapiens
  • Escherichia coli

Quick links

Citations

9 review citations

Integrative overview of antibodies against SARS-CoV-2 and their possible applications in COVID-19 prophylaxis and treatment.
Valdez-Cruz et al. (2021)
8 more

7 mentions without citation

Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering.
Verkhivker G. (2022)
6 more